This experiment tests the consequence of a mutation at the FatB gene in the wound-response of Arabidopsis. The FatB mutant allele (fatb KD J. (Plant Cell 2003, Vol 15, 1020-1033)) was obtained from Dr. Katayonn Dehesh, of California, Davis, Davis, CA. This allele is in the Ws background.The growth conditions are as follows: 1. Seeds (between 14 and 16) are sown on in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue Seeds were arranged on the plates in a single horizontal line at the 1-cm mark the top of the plate.2. Each plate contains between 20 and 25-ml of sterile MS containing 0.1% (w/v) sucrose.3. Prior to sowing, seeds were sterilized by for 1 minute at room temperature with a 300-l solution of 50% (v/v) ethanol, solution was removed and replaced with a 300-l solution consisting of 1% (v/v) 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution and incubated at room temperature for 10-minutes. The seeds were then washed three changes of 0.3-ml of sterile water.
Lipidomics studies on NIDDK / NIST human plasma samples
STUDY_TYPE
MS analysis on human plasma
STUDY_SUMMARY
The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) in with the National Institute of Standards (NIST) recently produced a human standard reference material (SRM 1950) for metabolite analysis. The SRM was by obtaining plasma samples from 100 individuals between 40 and 50 years of whose ethnicity was representative of the US population and that included an number of men and women. The intent of the NIDDK/NIST project was to provide a material that would be publically available to researchers and that could be by the clinical chemistry community to identify plasma metabolites for purposes. Signature metabolites could then be further probed for their as disease biomarkers. The LIPID MAPS Consortium has undertaken the task to this SRM by systematically identifying and quantifying the lipid molecular in the six main categories of mammalian lipids. The quantitative levels of over different lipids present in this reference human plasma sample are presented
Timecourse on RAW 264.7 cells treated with Kdo2-Lipid A and compactin
STUDY_TYPE
Timecourse experiment
STUDY_SUMMARY
Lipidomics studies on macrophages - RAW 264.7 cells treated with Kdo2-Lipid A compactin. Experiments were conducted with RAW264.7 cells fed 10% fetal calf 8-timepoint study: Measurements were taken at 0, 0.5,1,2,4,8, 12, and 24hrs (i) compactin, (ii) Kdo2-Lipid A, (iii) compactin + Kdo2-Lipid A. and (iv)
In this study, seventeen white wines including Chardonnays, Viogniers, Pinot gris, Rieslings and Sauvignon blancs (which were part of a M.S. study in the Viticulture & Enology Department on white wine mouthfeel properties), were analyzed by GC-TOF. Additionally, chemical data obtained will be mined with the sensory data collected to further investigate the chemical basis for mouthfeel properties in wine.
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), rise to devastating crop losses in rice. Disease resistant rice cultivars are most economical way to combat the disease. The TP309 cultivar is susceptible to by Xoo strain PXO99. A transgenic variety, TP309_Xa21, expresses the pattern receptor Xa21, and is resistant. PXO99?raxST, a strain lacking the raxST gene, able to overcome Xa21-mediated immunity. We used a single extraction solvent to comprehensive metabolomics and transcriptomics profiling under sample limited and analyze the molecular responses of two rice lines challenged with either or PXO99?raxST. LCTOF raw data file filtering resulted in better within group of replicate samples for statistical analyses. Accurate mass match compound with molecular formula generation (MFG) ranking of 355 masses was achieved with METLIN database. GCTOF analysis yielded an additional 441 compounds after database processing, of which 154 were structurally identified by retention library matching. Multivariate statistics revealed that the susceptible and genotypes possess distinct profiles. Although few mRNA and metabolite were detected in PXO99 challenged TP309 compared to mock, many differential occurred in the Xa21-mediated response to PXO99 and PXO99?raxST. Acetophenone, fatty acids, alkaloids, glutathione, carbohydrate and lipid biosynthetic were affected. Significant transcriptional induction of several pathogenesis genes in Xa21 challenged strains, as well as differential changes to GAD, PAL, and Glutathione-S-transferase transcripts indicated limited correlation with changes under single time point global profiling conditions.
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
This experiment tests the effect of individual mutations on the metabolome of The standardized growth conditions are as follows: 1. Seeds (between 14 and 16) sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher catalogue #08-757-11A). Seeds were arranged on the plates in a single line at the 1-cm mark from the top of the plate. 2. Each plate contains between and 25-ml of sterile MS media containing 0.1% (w/v) sucrose. 3. Prior to seeds were sterilized by treating for 1-minute at room temperature with a 300-l of 50% (v/v) ethanol, this solution was removed and replaced with a 300-l consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and (v/v) bleach solution (Clorox), and incubated at room temperature for The seeds were then washed with three changes of 0.3-ml of sterile water. 4. sowing with seeds, the plates were wrapped with Micropore tape (3M Health Care, #1530-0), and then stored horizontally for 4-days at 4 °C, with of 1 mol/m2. 5. On the 5th day, plates were moved to the growth room, and held a vertical position in Plexi-glass holders for 17-days this growth room is labeled in Table I. 6. On 18th day Petri plates were opened and the aerial of these plants were harvested immediately upon plate opening. 7. Upon plant material was quenched by immersion in liquid nitrogen and stored at 70
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
To determine the basis of running capacity and health differences in outbread N/NIH rats selected for high capacity (HCR) and low capacity (LCR) running (a for VO2max) (see:Science. 2005 Jan 21;307(5708):418-20). Plasma collected at 12 of age in generation 28 rats after ad lib feeding or 40% caloric restriction at week 8 of age. All animals fasted 4 hours prior to collection between 5-8
Determine purity and quality of IROA labelled glucose
STUDY_TYPE
NMR and MS analysis
STUDY_SUMMARY
We demonstrate the global metabolic analysis ofCaenorhabditis elegansstress using a mass-spectrometry-based technique called isotopic ratio outlier (IROA). In an IROA protocol, control and experimental samples are isotopically with 95 and 5%13C, and the two sample populations are mixed together for extraction, sample preparation, and LC-MS analysis.To illustrate the utility of for global metabolomics, we exposed wild-type (N2) worms to a heat shock (30 heat shock at 33 C), which causes significant, widespread changes in We collected and analyzed material from the exometabolome (all material that release in the supernatant) and the endometabolome (homogenized total extracts the worm bodies).
INSTITUTE
University of Florida
DEPARTMENT
Biochemistry & Molecular Biology
LAST_NAME
Stupp
FIRST_NAME
Gregory
ADDRESS
-
EMAIL
stuppie@ufl.edu
PHONE
-
STUDY_COMMENTS
Determine purity and quality of IROA labelled glucose
The goal of the study was to determine whether there is a set of metabolites that differentiate people who have knee OA and show radiographic disease progression over 18 months from those who have knee OA and do not show disease progression over the same time period.
This metabolomics pilot and feasibility (P & F) study was conducted to provide data to be used to gain a better understanding of metabolic alterations in people with knee osteoarthritis (OA) and to discover novel biomarkers of the disease. The goal of the metabolomics study was to determine if metabolic differences, detected by a comprehensive metabolomics analysis, can be used to distinguish people who will develop symptomatic knee OA from those who will not. For this metabolomics study, individuals participating in T1 or T1* with 5-year follow-up at T2 were selected. At T2 subjects were on average 68.1(9.12) years old with an average BMI of 31.4(7.01) with 32% men and one-third African American. All had weight-bearing posterior-anterior knee films obtained with the Synaflexer positioning device at both time points and read paired for Kellgren-Lawrence grade and minimum joint space. Urine samples (second morning void) collected from 36 overweight or obese participants in the JoCo at T1 or T1* were selected from two subgroups (a group that developed radiographic osteoarthritis (n=16) and an age, race, sex, and BMI matched group that did not develop osteoarthritis (n=20). Radiographic knee OA was defined as Kellgren-Lawrence grade 2-4 at T2 in a person with Kellgren-Lawrence grade 0 or 1 at T1 or T1*.
Metabolomics Analysis of Thermally Challenged Mayfly Larvae (GCMS analysis)
STUDY_TYPE
Metabolomic analysis of mayflies
STUDY_SUMMARY
The purpose of this study was to examine the metabolic profiles of mayfly triangulifer) larvae subjected to thermal challenge. This species is unusual in of its ease of culture, and its suitability as a laboratory test organism. Our here was to examine how an environmentally realistic thermal challenge affects physiology of this organism. In this study, we obtained several types of insect and we were able to show that GC-MS Metabolomics could be used to distinguish the different types of larvae.
Metabolomics Involved in Early Life Antibiotic Exposures(DuraSTAT-Cecal)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the DuraSTAT sub-study, a total of 18 samples from 8 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were given STAT penicillin and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a high fat diet.
Metabolomics Involved in Early Life Antibiotic Exposures(DuraSTAT-Liver)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the DuraSTAT sub-study, a total of 18 samples from 8 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were given STAT penicillin and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a high fat diet.
Metabolomics Involved in Early Life Antibiotic Exposures(DuraSTAT-Urine)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the DuraSTAT sub-study, a total of 18 samples from 8 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were given STAT penicillin and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a high fat diet.
Metabolomics Involved in Early Life Antibiotic Exposures(TranSTAT-Cecal)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the TranSTAT sub-study, a total of 18 samples from 8 week old, female Swiss webster mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were inoculated with cecal contents from STAT mice and 3 mice/matrix were inoculated with cecal contents from Control mice. The mice were housed with conventional bedding and fed a high fat diet.
Metabolomics Involved in Early Life Antibiotic Exposures(TranSTAT-Liver)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the TranSTAT sub-study, a total of 18 samples from 8 week old, female Swiss webster mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were inoculated with cecal contents from STAT mice and 3 mice/matrix were inoculated with cecal contents from Control mice. The mice were housed with conventional bedding and fed a high fat diet.
Metabolomics Involved in Early Life Antibiotic Exposures(TranSTAT-Serum)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the TranSTAT sub-study, a total of 18 samples from 8 week old, female Swiss webster mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were inoculated with cecal contents from STAT mice and 3 mice/matrix were inoculated with cecal contents from Control mice. The mice were housed with conventional bedding and fed a high fat diet.
Metabolomics Involved in Early Life Antibiotic Exposures(NOD-Cecal)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the NOD sub-study, a total of 18 samples from 6 week old, male NOD/ShiLtj mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were exposed to PAT and 3 mice/matrix were non-exposed Controls. The mice were housed with SPF (Helicobacter neg/MNV neg) bedding and fed a normal diet.
Metabolomics Involved in Early Life Antibiotic Exposures(NOD-Liver)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the NOD sub-study, a total of 18 samples from 6 week old, male NOD/ShiLtj mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were exposed to PAT and 3 mice/matrix were non-exposed Controls. The mice were housed with SPF (Helicobacter neg/MNV neg) bedding and fed a normal diet.
Metabolomics Involved in Early Life Antibiotic Exposures(NOD-Serum)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the NOD sub-study, a total of 18 samples from 6 week old, male NOD/ShiLtj mice; comprised of 6 serum samples, 6 cecal content samples and 6 liver tissue samples were analyzed. Three mice/matrix were exposed to PAT and 3 mice/matrix were non-exposed Controls. The mice were housed with SPF (Helicobacter neg/MNV neg) bedding and fed a normal diet.
Metabolomics Involved in Early Life Antibiotic Exposures(EstroSTAT-Liver )
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the EstroSTAT sub-study, a total of 18 samples from 23 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 serum samples and 6 liver tissue samples were analyzed. Three mice/matrix were given STAT penicillin and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a Low phyto-estrogen diet.
Metabolomics Involved in Early Life Antibiotic Exposures(EstroSTAT-Serum)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the EstroSTAT sub-study, a total of 18 samples from 23 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 serum samples and 6 liver tissue samples were analyzed. Three mice/matrix were given STAT penicillin and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a Low phyto-estrogen diet.
Metabolomics Involved in Early Life Antibiotic Exposures(EstroSTAT-Urine)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the EstroSTAT sub-study, a total of 18 samples from 23 week old, female C57BL/6 mice; comprised of 6 urine samples, 6 serum samples and 6 liver tissue samples were analyzed. Three mice/matrix were given STAT penicillin and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a Low phyto-estrogen diet.
Metabolomics Involved in Early Life Antibiotic Exposures(VGSTAT-Cecal)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the VG STAT sub-study, a total of 18 samples from 7 week old, male C57BL/6 mice; comprised of 9 cecal content samples and 9 liver tissue samples were analyzed. Three mice/matrix were given penicillin VK, 3 were given penicillin G, and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a normal diet.
Metabolomics Involved in Early Life Antibiotic Exposures(VGSTAT-Liver)
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
In the VG STAT sub-study, a total of 18 samples from 7 week old, male C57BL/6 mice; comprised of 9 cecal content samples and 9 liver tissue samples were analyzed. Three mice/matrix were given penicillin VK, 3 were given penicillin G, and 3 mice/matrix were non-treated Controls. The mice were housed with conventional bedding and fed a normal diet.
Human subjects were given high PUFA diet for 21 days then converted to high diet for another 21 days. Plasma samples were drawn during the feeding process 7 visits.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Plasma metabolomics: Comparison of non-diabetic controls with T1D patients
STUDY_TYPE
Drug effect study
STUDY_SUMMARY
Non-diabetic controls whose metabolites were compared to T1D patients with and insulin. Seven C-peptide?negative T1D subjects were studied on two occasions: during insulin treatment and the other following withdrawal of insulin for 8 h compared with matched healthy ND participants
Identification of altered metabolic pathways in Alzheimer's disease, mild impairment and cognitively normals using Metabolomics (plasma)
STUDY_TYPE
1
STUDY_SUMMARY
Criteria for the diagnosis of amnestic MCI included: (i) memory complaint by the patient and collateral source; (ii) impairment in 1 or more of the 4 domains (memory, executive functioning/attention, visuospatial, or language); essentially normal functional activities of daily living; and (iv) absence of In general, the amnestic MCI determination is made when the memory measures 1.0â??1.5 SD below the means for age and education appropriate individuals our community; however, rigid cutoffs on psychometric scores were not used to the diagnosis of amnestic MCI which was made on clinical grounds. The diagnosis dementia was made using DSM-IV criteria, and the diagnosis of AD was made using criteria. Subjects were considered to be CN if they performed within the range and did not meet criteria for MCI or dementia.
Identification of altered metabolic pathways in Alzheimer's disease, mild impairment and cognitively normals using Metabolomics (CSF)
STUDY_TYPE
MS
STUDY_SUMMARY
Criteria for the diagnosis of amnestic MCI included: (i) memory complaint by the patient and collateral source; (ii) impairment in 1 or more of the 4 domains (memory, executive functioning/attention, visuospatial, or language); essentially normal functional activities of daily living; and (iv) absence of In general, the amnestic MCI determination is made when the memory measures 1.0?1.5 SD below the means for age and education appropriate individuals in community; however, rigid cutoffs on psychometric scores were not used to the diagnosis of amnestic MCI which was made on clinical grounds. The diagnosis dementia was made using DSM-IV criteria, and the diagnosis of AD was made using criteria. Subjects were considered to be CN if they performed within the range and did not meet criteria for MCI or dementia.
Metabolomic & lipidomic profiles in response to exogenous insulin & GLP-1 during prolonged fasting (GCMS)
STUDY_TYPE
Timecourse
STUDY_SUMMARY
This application requests funding to access state-of-the-art metabolomics and platforms at the NIH West Coast Metabolomics Center to analyze plasma samples recent insulin and glucagon-like peptide-1 (GLP-1) infusion experiments in prolong-fasted elephant seals. This suite of studies was designed to better the mechanisms contributing to the onset of an insulin resistantlike condition by prolonged food deprivation/starvation in mammals. Because elephant seals evolved robust physiological mechanisms that have allowed them to naturally such protracted bouts of fasting, they provide an ideal model to address our hypothesis that increased lipid utilization late in the fast contributes to resistance in elephant seals. Insulin resistance is a common consequence of in mammals and, while the mechanisms by which it manifests are still unclear, a shift favoring increased mobilization and utilization of lipids during food deprivation may be a principal causative factor. Insulin resistance has a connotation due to its association with obesity and diabetes among humans, but has been suggested to be an adaptive response to food deprivation.
INSTITUTE
University of California, Davis
DEPARTMENT
GBSF
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
451 Health Sci Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
1-530-752-8258
NUM_GROUPS
5
TOTAL_SUBJECTS
117
STUDY_COMMENTS
5 general classes are designed in the experiment:#1 - A=No GLP1/ Late GTT#2 - (Low Dose)#3 - C=GLP1 (High Dose)#4 - IL- Early Fasting Insulin Infusion#5 - Late Fasting Insulin InfusionEach of the 5 classes has 6 timepoints (5x6):T1 - minT2 - 10 minT3 - 30 minT4 - 60 minT5 - 120 minEach timepoint had 5 animals (5 x 5 classes x 6 timepoints = 150 totalBecause certain animals and timepoints to be excluded 108 measurments remain.The experiment also contains 9 technical of pooled samples (pool)The total sample number is 108 (biological) + 9 pooled = 117
Brophy and Askenazi hypothesize that postnatal renal maturation results in specific identifiable patterns of urinary metabolites and that these profiles will be altered in the presence of AKI. Their long-term goal is to identify novel metabolomics urinary profiles that can provide real-time evidence of evolving neonatal renal injury thereby allowing earlier diagnosis and treatment.This study includes 40 pre-term infants age 2 days. Twenty infants were identified as not having AKI (11 females, mean gestational age=182.8 days, mean birth weight=834.0 grams) and 20 infants were identified as having AKI (13 females, mean gestational age=183.9 days, mean birth weight=815.8 grams). There are no statistical differences between the two groups based on gender, gestational age, and birth weight.
INSTITUTE
RTI International
DEPARTMENT
RTI RCMRC
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 East Cornwallis Road, Research Triangle Park, NC 27709, USA.
Fetal metabolomic signature of exposure to iAs during pregnancy
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
This metabolomics pilot study was aimed to identify a fetal metabolomic signature of exposure to iAs during pregnancy. Fetal cord blood serum was collected immediately after delivery from a saline cleaned umbilical cord using an anticoagulant-free vacutainer tube, after clot formation the tube was centrifuged at 1200 rpm and the serum was collected and stored at -70°C. A subset of 50 cord serum samples were selected from the larger BEAR cohort to represent a wide range of iAs exposure as determined by iAs in drinking water (DW-iAs). The exposure during pregnancy was confirmed using U-tAs. A total of 50 cord blood serum samples were used in the metabolomics analysis The samples included 25 newborns with lower maternal iAs exposure levels (DW < 25?g As/L, mean U-tAs=16 ?g/L) and 25 newborns with higher maternal iAs exposure levels (DW> 25?g As/L, mean U-tAs =107 ?g/L).
INSTITUTE
RTI International
DEPARTMENT
Systems and Translational Sciences (STS)
LABORATORY
RTI RCMRC
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 East Cornwallis Roadm Research Triangle Park, NC 27709, USA
Metabolic Microenvironments in Normal Breast and Breast Cancer (MS analysis)
STUDY_TYPE
Metabolomic analysis of normal breast tissue
STUDY_SUMMARY
The purpose of this study was to understand the metabolomic changes in a breast microenvironment at various stages of cancer development and progression (i.e. breast, DCIS, and invasive cancer). The goal of this metabolomics pilot and study was to apply a broad spectrum GC-MS metabolomics method to determine changes in normal tissue of women with cancer correlate with progression and or subtype of the disease.
Effect of kinase inhibitors on FLT3-ITD AML cell metabolomes
STUDY_TYPE
Metabolomics analysis on the effect of kinase inhibitors on FLT3-ITD AML cell to identify changes in cell signaling networks
STUDY_SUMMARY
FLT3-ITD AML cells (MR2) obtained from mice were treated with two MEK kinase (GSK and AZD) at 10 uM versus media only control. Conditioned media aliquots cellular fractions comprised of two aliquots (tecnical replicates) for LC-MS and one for Western blot analyses were collected at 0, 4, 24, and 48 hours. The was repeated three times. HPLC-MS data were acquired for 24 samples from one experiment.
Environmental impact on metabolomics and food allergy
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
This metabolomics pilot and feasibility (P&F) was conducted to determine if varying the levels of environmental LPS exposure and immunization with the vaccine adjuvant alum alters host metabolism. Additionally, the metabolomics will identify biomarkers that can predict allergic disease development and or disease severity after a peanut challenge in hypersensitive mice. Information gained from the proposed studies may allow for the identification of individuals who are at risk or not at risk for the development of allergic disease. Furthermore, completion of these studies may lead to identification of biological targets that may be used to develop novel therapies to treat or prevent allergic disease via future funding.
Combined Metabolomics and Lipidomics of Type 1 Diabetes (GCMS)
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Bell (University of Chicago) and collaborator Manami Hara uses a multi-omics to investigate the metabolome (primary metabolites), lipidome (complex lipids) signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice were assessed as diabetic or non-diabetic based on their fasting (4hr) blood levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and normoglycemic animals. The primary objective of this study was to identify biomarkers associated with beta-cell destruction/survival and T1D progression.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolite changes associated with methionine stress sensitivity of cancer (GC MS analysis)
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Kaiser (UC Irvine), aims to achieve understanding of a unique metabolic of cancer cells to explore development of novel unconventional therapeutic that exploit dependence of cancer cells on methyl-donor abundance. The past few have highlighted the role of altered metabolism in cancer. While mechanistic into changed metabolism in cancer is very limited, the importance of the pathway surrounding homocysteine and methionine for cancer cell proliferation been known for over 30 years.These findings, generally summarized as or methionine stress sensitivity, describe the phenomenon that most cancer cannot proliferate in growth medium where the amino acid methionine is replaced its direct metabolic precursor homocysteine. Importantly, non-tumorigenic cells unaffected by replacing methionine with homocysteine in the growth medium. For past years we have been studying methionine dependence of breast and prostate and demonstrated that methionine-dependence is caused by insufficient flux this pathway to sustain synthesis of the downstream metabolite and the methyl-donor S-adenosylmethionine (SAM).We have isolated rare cell clones from breast cancer cells (referred to as MB468RES) that are no longer methionine and proliferate in homocysteine medium. Interestingly, MB468RES have lost their for anchorage independent growth, a hallmark of cancer. The MB468 and MB468RES line pair confirms other observations showing that methionine dependence is linked to tumorigenicity. Importantly, this cell line pair is an ideal model to metabolite signatures linked to cancer cell methionine dependence. We propose characterize the metabolic changes triggered by the shift from normal growth to homocysteine medium in MB468 breast cancer cells and the methionine stress MB468RES derivatives. In addition we have developed cancer cell lines with shRNAs targeting methionine adenosyltransferase (MAT), the enzyme catalyzing of SAM from methionine and ATP. Inducible knockdown of MAT allows us to reduce SAM synthesis. Our previous results suggest that SAM limitation is the trigger for cancer cell methionine dependence. Thus metabolite profiling using MAT knockdown system will provide an independent dataset that together with profiles from the MB468 and MB468RES cell line pair will define critical profiles related to cancer cell methionine dependence. In the current untargeted analysis of primary metabolites and complex lipids, coupled with analysis of methionine pathway intermediates (folate and respective s-adenosylmethoinine, s-adenosylhomocysteine, choline, betaine) and metabolic will be conducted on MB468, MB468RES and MB468shRNA following the switch from containing media to homocysteine containing media over the course of 0, 2, 4, 12, 24 and 48 hours. The primary objectives were to 1) characterize the response to methionine stress and SAM limitation and 2) correlate the metabolic with cancer cell proliferation arrest and death.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: GC-TOF MS analyis of subcutaneous and visceral adipose tissue samples
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Biomarkers for Depression in Human Plasma in a Population Sample
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Roel Ophoff (UC Los Angeles ) and Steve Horwath (UC Los Angeles ) . Major disorder (MDD) is one of the most debilitating disorders in the United States a 12-month prevalence of 6.7% in the adult population. The disorder affects of Americans daily and is a major health concern with enormous economic cost society at large. Criteria for MDD diagnosis and treatment are based on various and symptoms not always fitting into strict diagnostic categories such as Despite various known risk factors (such as family history, age, and gender), markers supporting diagnosis or prediction of MDD are unavailable. We have cerebrospinal fluid (CSF) and peripheral blood of more than 600 subjects from general population. For each of the participants we also obtained biometric as well as behavioral trait measures. One of the measures is the Beck Inventory (BDI), a well-established questionnaire for measuring severity of Based on the BDI, roughly 5% of participants suffer from severe depressive while most of these subjects are not under treatment or receiving any for depression In the current investigation, untargeted analysis of primary was conducted on age and gender matched human cerebrospinal fluid (CSF) and from subjects suffering with MDD ( n=50) and control subjects (n=50). were diagnosed as having MDD based on the Beck Depression Inventory.The primary of this study were to 1) identify metabolites which discriminate between with and without depression symptoms in the CSF and plasma and 2) how changes between CSF and plasma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Biomarkers for Depression in Human Cerebrospinal Fluid in a Population Sample
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Roel Ophoff (UC Los Angeles ) and Steve Horwath (UC Los Angeles ) . Major disorder (MDD) is one of the most debilitating disorders in the United States a 12-month prevalence of 6.7% in the adult population. The disorder affects of Americans daily and is a major health concern with enormous economic cost society at large. Criteria for MDD diagnosis and treatment are based on various and symptoms not always fitting into strict diagnostic categories such as Despite various known risk factors (such as family history, age, and gender), markers supporting diagnosis or prediction of MDD are unavailable. We have cerebrospinal fluid (CSF) and peripheral blood of more than 600 subjects from general population. For each of the participants we also obtained biometric as well as behavioral trait measures. One of the measures is the Beck Inventory (BDI), a well-established questionnaire for measuring severity of Based on the BDI, roughly 5% of participants suffer from severe depressive while most of these subjects are not under treatment or receiving any for depression In the current investigation, untargeted analysis of primary was conducted on age and gender matched human cerebrospinal fluid (CSF) and from subjects suffering with MDD ( n=50) and control subjects (n=50). were diagnosed as having MDD based on the Beck Depression Inventory.The primary of this study were to 1) identify metabolites which discriminate between with and without depression symptoms in the CSF and plasma and 2) how changes between CSF and plasma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: GC-TOF MS analyis of serum samples
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolomic profiling of influenza: a 2009 pandemic H1N1 influenza in lean and mice (via blood and tissue)
STUDY_TYPE
Metabolomics analysis on the effec of diet-related obesity on the immune to pH1N1 infection
STUDY_SUMMARY
Lung samples were obtained at 15 weeks from 56 mice that had received either a low fat diet, or a high fat diet and that were uninfected, 4 days or 8 days post-infection.
Effect of diet and age on ovarian metabolome (via tissue)
STUDY_TYPE
Metabolomics analysis on the ovarian metabolome
STUDY_SUMMARY
Ovarian samples from twenty-one adult, female Cynomolgus monkeys were studied, of which were fed the Western #907 diet, and 13 of which were fed the Prudent diet. HPLC-MS data were acquired for the 21 samples.
Effect of diet and age on ovarian metabolome (serum metabolome compared to
STUDY_TYPE
Metabolomics analysis on the serum metabolome for comparison against the metabolome
STUDY_SUMMARY
Serum samples from twenty-one adult, female Cynomolgus monkeys were studied, of which were fed the Western #907 diet, and 13 of which were fed the Prudent diet. HPLC-MS data were acquired for the 21 samples.
Genetic effects of high fat diet on mouse fecal metabolomics
STUDY_TYPE
Metabolomics analysis on the effect of genetics and diet on the metabolism of GI tract and obesity
STUDY_SUMMARY
This study includes 72 female mice with 4 mice from each of the 18 mice Two mice from each strain were fed a high fat diet and two mice were fed a fat diet. The 36 mice fed a normal fat diet will serve as the controls. All are age 27.6 weeks or older at the time of sacrifice. UPLC-MS data was for all 72 samples.
Combined Metabolomics and Lipidomics of Type 1 Diabetes (QTOF)
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Bell (University of Chicago) and collaborator Manami Hara uses a multi-omics to investigate the metabolome (primary metabolites), lipidome (complex lipids) signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice were assessed as diabetic or non-diabetic based on their fasting (4hr) blood levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and normoglycemic animals. The primary objective of this study was to identify biomarkers associated with beta-cell destruction/survival and T1D progression.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolite changes associated with methionine stress sensitivity of cancer (CSH MS analysis)
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Peter Kaiser (UC Irvine), aims to achieve understanding of a unique metabolic dependence of cancer cells to explore development of novel unconventional therapeutic strategies that exploit dependence of cancer cells on methyl-donor abundance. The past few years have highlighted the role of altered metabolism in cancer. While mechanistic insight into changed metabolism in cancer is very limited, the importance of the metabolic pathway surrounding homocysteine and methionine for cancer cell proliferation has been known for over 30 years. These findings, generally summarized as methionine-dependence or methionine stress sensitivity, describe the phenomenon that most cancer cells cannot proliferate in growth medium where the amino acid methionine is replaced with its direct metabolic precursor homocysteine. Importantly, non-tumorigenic cells are unaffected by replacing methionine with homocysteine in the growth medium. For the past years we have been studying methionine dependence of breast and prostate cancer and demonstrated that methionine-dependence is caused by insufficient flux through this pathway to sustain synthesis of the downstream metabolite and the principal methyl-donor S-adenosylmethionine (SAM). We have isolated rare cell clones from MDA-MB468 breast cancer cells (referred to as MB468RES) that are no longer methionine dependent and proliferate in homocysteine medium. Interestingly, MB468RES have lost their ability for anchorage independent growth, a hallmark of cancer. The MB468 and MB468RES cell line pair confirms other observations showing that methionine dependence is tightly linked to tumorigenicity. Importantly, this cell line pair is an ideal model to identify metabolite signatures linked to cancer cell methionine dependence. We propose to characterize the metabolic changes triggered by the shift from normal growth medium to homocysteine medium in MB468 breast cancer cells and the methionine stress insensitive MB468RES derivatives. In addition we have developed cancer cell lines with inducible shRNAs targeting methionine adenosyltransferase (MAT), the enzyme catalyzing synthesis of SAM from methionine and ATP. Inducible knockdown of MAT allows us to specifically reduce SAM synthesis. Our previous results suggest that SAM limitation is the critical trigger for cancer cell methionine dependence. Thus metabolite profiling using the MAT knockdown system will provide an independent dataset that together with metabolite profiles from the MB468 and MB468RES cell line pair will define critical metabolic profiles related to cancer cell methionine dependence. In the current investigation, untargeted analysis of primary metabolites and complex lipids, coupled with quantitative analysis of methionine pathway intermediates (folate and respective derivatives, s-adenosylmethoinine, s-adenosylhomocysteine, choline, betaine) and metabolic flux will be conducted on MB468, MB468RES and MB468shRNA following the switch from methionine containing media to homocysteine containing media over the course of 0, 2, 4, 8, 12, 24 and 48 hours. The primary objectives were to 1) characterize the metabolic response to methionine stress and SAM limitation and 2) correlate the metabolic signatures with cancer cell proliferation arrest and death.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: UHPLC-QTOF MS analyis of subcutaneous and visceral adipose tissue
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.Â
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
59
STUDY_COMMENTS
Lipidomics profiles for studyThis is the SAT and VAT part of the studyLabel-ID conserved for all parts of the study---The samples had to be diluted for mode measurements (therefore 2 dilutions are measured for the same sample). are then combined and scaling factor is used for final results.
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: UHPLC-QTOF MS analyis of serum samples
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
1
TOTAL_SUBJECTS
59
STUDY_COMMENTS
Lipidomics profiles for studyThis is the serum part of the studyLabel-ID os for all parts of the study---
A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Infection
STUDY_TYPE
Timecourse of Infection
STUDY_SUMMARY
The potential for commensal microorganisms indigenous to a host (the or microbiota) to alter infection outcome by influencing host-pathogen is largely unknown. We used a multi-omics systems approach, proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular between the murine host, the pathogen Salmonella enterica serovar Typhimurium Typhimurium), and commensal gut microorganisms during intestinal infection with Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while growth of Salmonella and Enterococcus). Alteration of the host microbiome structure was highly correlated with gut environmental changes, including the of metabolites normally consumed by commensal microbiota. Finally, the less phase of S. Typhimuriums lifecycle was investigated, and both proteomic and evidence suggests S. Typhimurium may take advantage of increased fucose to metabolize fucose while growing in the gut. The application of multiple measurements to Salmonella-induced intestinal inflammation provides insights complex molecular strategies employed during pathogenesis between host, and the microbiome.
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of activation
STUDY_TYPE
growth condition, timecourse
STUDY_SUMMARY
Macrophages are central players in immune response, manifesting divergent to control inflammation and innate immunity through release of cytokines and signaling factors. Recently, the focus on metabolism has been reemphasized as signaling and regulatory pathways of human pathophysiology, ranging from cancer aging, often converge on metabolic responses. Here, we used genome-scale and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to metabolic features that are critical for macrophage activation. A genome-scale network for the RAW 264.7 cell line was constructed to determine metabolic of activation. Metabolites well-known to be associated with immunoactivation and arginine) and immunosuppression (tryptophan and vitamin D3) were among the critical effectors. Intracellular metabolic mechanisms were assessed, a suppressive role for de-novo nucleotide synthesis. Finally, underlying mechanisms of macrophage activation were identified by analyzing multi-omic obtained from LPS-stimulated RAW cells in the context of our flux-based This study demonstrates that the role of metabolism in regulating activation be greater than previously anticipated and elucidates underlying connections activation and metabolic effectors. This submission corresponds to the data from this study.
Salmonella Modulates Metabolism during Growth under Conditions that Induce of Virulence Genes
STUDY_TYPE
growth conditions, timecourse
STUDY_SUMMARY
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative that uses complex mechanisms to invade and proliferate within mammalian host To investigate possible contributions of metabolic processes to virulence in S. grown under conditions known to induce expression of virulence genes, we used a systems biology approach coupled with genome scale modeling. First, we distinct metabolite profiles associated with bacteria grown in either rich or media and report the most comprehensive coverage of the S. Typhimurium to date. Second, we applied an omics-informed genome scale modeling analysis of functional consequences of adaptive alterations in S. Typhimurium metabolism growth under our conditions. Modeling efforts highlighted a decreased cellular to both produce and utilize intracellular amino acids during stationary phase in virulence conditions, despite significant abundance increases for these as observed by our metabolomics measurements. Furthermore, analyses of omics in the context of the metabolic model indicated rewiring of the metabolic to support pathways associated with virulence. For example, cellular of polyamines were perturbed, as well as the predicted capacity for secretion uptake.
A study of changes in lipid metabolism of ovarian cancer cells co-cultured with GC-TOF MS analysis
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Ernst Lengyel (University of Chicago).The biology of ovarian cancer (OvCa) is distinct from that of most epithelial tumors, in that hematogenous metastases rare, and ovarian tumors remain confined to the peritoneal cavity. The omentum, large pad of fat tissue (20x13x3cm) covering the bowel, is the most common site OvCa metastasis. It consists primarily of adipocytes, which become the microenvironment for the OvCa cells. The underlying hypothesis for this is that, in the presence of adipocytes, the metabolism of OvCa cells is and shifts towards lipid utilization, which provides energy that facilitates growth and metastasis. Preliminary results suggest that primary human omental secrete cytokines which promote the metastasis of OvCa cells to the omentum and subsequent invasion. Once metastasis has occurred, OvCa cells induce lipolysis omental adipocytes, and use the energy derived from these lipids to study the metabolic changes in the tumor microenvironment we have established a organotypic culture of the human omentum using primary human cells established patient tissue. Metabolic studies will be performed on adipocytes and OvCa individually, on conditioned media and on adipocytes and OvCa cells co-cultured our 3D model, with the goal of arriving at a comprehensive analysis of primary and lipids in the tumor microenvironment.In the current investigation, analysis of primary metabolites and complex lipids were conducted on adipocytes OvCa cells individually, on conditioned media and on adipocytes and OvCa cells in our 3D model. Analysis of oxylipins was conducted on conditioned media. To better understanding of the dynamic regulation of metabolic pathways we will perform metabolic flux analysis using labeled cells (13C-glucose, in the 3D culture model.The primary objective of this study is to gain insight the dynamic interactions between OvCa cells and human adipocytes with the of elucidating targets of therapeutic intervention.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
14
STUDY_COMMENTS
Lipidomics profiles for studyFor the co-culture Human Adipocytes were grown in of SKOV3ip1 ovarian cancer cellsFor control samples the adipocytes were grown the absence of SKOV3ip1 ovarian cancer cells---Exp design 2 x 14Final result is by merging results from both files and applying dilution factor.Reason was high concentration in positive mode onlyRaw Data File (Positive Mode_TGs) Data File (Positive Mode_Non-TGs) (dilution2)
A study of changes in lipid metabolism of ovarian cancer cells co-cultured with UHPLC-QTOF MS analysis
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Ernst Lengyel (University of Chicago).The biology of ovarian cancer (OvCa) is distinct from that of most epithelial tumors, in that hematogenous metastases rare, and ovarian tumors remain confined to the peritoneal cavity. The omentum, large pad of fat tissue (20x13x3cm) covering the bowel, is the most common site OvCa metastasis. It consists primarily of adipocytes, which become the microenvironment for the OvCa cells. The underlying hypothesis for this is that, in the presence of adipocytes, the metabolism of OvCa cells is and shifts towards lipid utilization, which provides energy that facilitates growth and metastasis. Preliminary results suggest that primary human omental secrete cytokines which promote the metastasis of OvCa cells to the omentum and subsequent invasion. Once metastasis has occurred, OvCa cells induce lipolysis omental adipocytes, and use the energy derived from these lipids to study the metabolic changes in the tumor microenvironment we have established a organotypic culture of the human omentum using primary human cells established patient tissue. Metabolic studies will be performed on adipocytes and OvCa individually, on conditioned media and on adipocytes and OvCa cells co-cultured our 3D model, with the goal of arriving at a comprehensive analysis of primary and lipids in the tumor microenvironment.In the current investigation, analysis of primary metabolites and complex lipids were conducted on adipocytes OvCa cells individually, on conditioned media and on adipocytes and OvCa cells in our 3D model. Analysis of oxylipins was conducted on conditioned media. To better understanding of the dynamic regulation of metabolic pathways we will perform metabolic flux analysis using labeled cells (13C-glucose, in the 3D culture model.The primary objective of this study is to gain insight the dynamic interactions between OvCa cells and human adipocytes with the of elucidating targets of therapeutic intervention.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
14
STUDY_COMMENTS
Lipidomics profiles for studyFor the co-culture Human Adipocytes were grown in of SKOV3ip1 ovarian cancer cellsFor control samples the adipocytes were grown the absence of SKOV3ip1 ovarian cancer cells---Exp design 2 x 14Final result is by merging results from both files and applying dilution factor.Reason was high concentration in positive mode onlyRaw Data File (Positive Mode_TGs) Data File (Positive Mode_Non-TGs) (dilution2)
Quantitative Metabolomics by 1H-NMR and LC-MS/MS Confirms Altered Metabolic in Diabetes
STUDY_TYPE
Pre- and Post- insulin study with matched controls
STUDY_SUMMARY
We obtained plasma samples from 7 c-peptide negative type 1 diabetic (T1D) and 7 non-diabetic controls (Con) that were matched for age (T1D = yrs, Con = 30.2±3.4 yrs), body mass (T1D = 80.2±4.7kg, Con = 81.9±7.4 kg) BMI (T1D = 26.5±1.2 kg/m2, Con = 25.2±1.3 kg/m2). Type 1 diabetic people were while treated with insulin and also after 8 hours of insulin deprivation
A statistical analysis of the effects of urease pre-treatment on the of the urinary metabolome by gas chromatographymass spectrometry
STUDY_TYPE
Analytical Comparison
STUDY_SUMMARY
Urease pre-treatment of urine has been utilized since the early 1960s to remove levels of urea from samples prior to further processing and analysis by gas spectrometry (GCMS). Aside from the obvious depletion or elimination of urea, effect, if any, of urease pre-treatment on the urinary metabolome has not been in detail. Here, we report the results of three separate but related that were designed to assess possible indirect effects of urease pre-treatment the urinary metabolome as measured by GCMS. In total, 235 GCMS analyses performed and over 106 identified and 200 unidentified metabolites were across the three experiments. The results showed that data from urease samples (1) had the same or lower coefficients of variance among reproducibly metabolites, (2) more accurately reflected quantitative differences and the ratios among different urine volumes, and (3) increased the number of identifications. Overall, we observed no negative consequences of urease In contrast, urease pre-treatment enhanced the ability to distinguish between and biological sample types compared to no treatment. Taken together, these show that urease pre-treatment of urine offers multiple beneficial effects that any artifacts that may be introduced to the data in urinary metabolomics
Metabolomics Analysis of Frontal Fibrosing Alopecia
STUDY_TYPE
Unaffected and Affected patient scalp biopsies
STUDY_SUMMARY
Scarring alopecia consists of a collection of disorders characterized by of hair follicles, replacement with fibrous scar tissue, and irreversible hair Alopecia affects men and women worldwide and can be a significant source of stress and depression for affected individuals. The purpose of this study was explore metabolic profiles in scalp tissue samples from normal control subjects and in matched samples obtained from affected (n=12) and unaffected (n=12) of the scalp in patients with lymphocytic Frontal Fibrosing Alopecia (FFA). fibrosing alopecia results from destruction of hair follicles by an lymphocytic infiltrate that is localized around the upper portion of the hair
INSTITUTE
Case Western Reserve University
DEPARTMENT
Dermatology
LABORATORY
Karnik Lab
LAST_NAME
Karnik
FIRST_NAME
Pratima
ADDRESS
-
EMAIL
psk11@case.edu
PHONE
216-368-0209
NUM_GROUPS
3 groups-Paired unaffected and affected (n=12),Normals(n=6)
TOTAL_SUBJECTS
Patients (N=12), Normals (N=6)
STUDY_COMMENTS
Affected scalp biopsies were obtained from frontal scalp, Unaffected from scalp. Normal scalp biopsies were obtained from the occipital scalp.
Dysfunctional lipid metabolism underlies the effect of perinatal DDT exposure the development of metabolic syndrome
STUDY_TYPE
Chemical dosage and feeding study
STUDY_SUMMARY
Targeted metabolomic analysis of bile acids was performed on 15 mouse liver collected from mice euthanized at 9 months following consumption of a high fat w/o perinatal DDT exposure. Funded by the National Institute of Health (R00 R03 DK082724, U24 DK092993, U24 DK097154, T32 ES007059, and P60 DK020541), the Diabetes Association, and USDA-ARS intramural Project 5306-51530-019-00D. were analyzed by UPLC-MS/MS using a Waters Acquity UPLC and detected on an API QTrap (AB Sciex, Framingham, MA, USA) by multiple reaction monitoring (MRM) negative mode electrospray ionization.
Two groups of mixtures with 5 replicates each were each made using 20 synthetic metabolites. Some metabolites were at equal concentrations in both groups, and 10 metabolites differed between groups with half higher in group A, and half higher in group B.
INSTITUTE
University of Florida
DEPARTMENT
Department of Biochemistry and Molecular Biology /SECIM
LABORATORY
Arthur Edison
LAST_NAME
Arthur
FIRST_NAME
Edison
ADDRESS
R3-226 Academic Research Building, Department of Biochemistry & Molecular Biology, PO Box 100245, Gainesville, FL 32610-0245
Cold adaptation shapes the robustness of metabolic networks in Drosophila melanogaster
STUDY_TYPE
Time course during cold exposure for four genetic lines of flies
STUDY_SUMMARY
Metabolites of cold hardy versus cold susceptible flies were compared using N less than R-based metabolomics. We used 8 replicates per line (2 hardy lines, two susceptible lines), and sampled each line at three time points (before, during and after cold), giving rise to 96 samples total.
Factors for Epigenetic Silencing of Lung Cancer Genes
STUDY_TYPE
Metabolomic analysis of Plasma
STUDY_SUMMARY
To test the hypothesis that the propensity for silencing of tumor suppressor genes in the respiratory epithelium of chronic smokers by promoter hypermethylation is influenced by sequence variations that modify the activity of genes and microRNAÕs that directly or indirectly influence de novo methylation and chromatin remodeling.
This experiment is investigating the metabolome of men, healthy women, and with Polycystic Ovary Syndrome (PCOS) with and without Obstructive Sleep Apnea
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomic and lipidomic profiles in response to exogenous insulin and GLP-1 during prolonged fasting
STUDY_TYPE
Timecourse
STUDY_SUMMARY
Seventeen northern elephant seal pups constituting four different cohorts at Nuevo State Reserve were studied at two post-weaning periods: early (1-2 wk weaning; n=5) and late (6-7 weeks post weaning; n=12). Study #1: Prior to each protocol, plasma U/kg). Following the infusion, blood samples were collected at determine the effects of prolonged fasting on peripheral insulin activity and samples were collected. Ten fasting seal pups (n=5 early, n=5 late) were (i.v.) with a mass-specific dose of insulin (0.065 U/kg). Following the blood samples were collected at 10, 30, 60, 90, and 120 minutes. Study #2: late-fasted seal pups were administered either a low (LDG; 10 pmol/kg; n=3) or (HDG; 100 pmol/kg; n=4) dose of GLP-1 immediately following a glucose bolus g/kg) (i.v.) infused within 2 mins. the infusions, blood samples were collected 10, 30, 60, 90, 120, and 150 minutes.
SIRM Analysis of human P493 cells under hypoxia in [U-13C/15N] labeled medium (Positive ion mode FTMS)
STUDY_TYPE
tracer
STUDY_SUMMARY
SIRM Analysis of MYC inducible P493 cells under normoxia and hypoxia in labeled Glutamine medium
INSTITUTE
University of Kentucky
DEPARTMENT
Toxicology
LAST_NAME
Fan
FIRST_NAME
Teresa
ADDRESS
-
EMAIL
twmfan@gmail.com
PHONE
-
NUM_GROUPS
4
TOTAL_SUBJECTS
8
STUDY_COMMENTS
For protocols and additional information, see Le, A., Lane, A.N., Hamaker, M., S., Barbi, J., Tsukamoto, T., Rojas, C.J., Slusher, B.S., Zhang, H., Zimmerman. Liebler, D.C., Slebos, R.J.C., Lorkiewicz, P.K., Higashi, R.M., Fan, T.W-M., Dang, C.V. Cell Metabolism 15, 110 (2012). 13C/15N Gln was used as the tracer this study, even though the analysis did not explicity look for 15N
Impact of insulin deprivation and treatment on sphingolipid distribution in muscle subcellular compartments of streptozotocin-diabetic C57Bl/6 mice
STUDY_TYPE
Insulin depravation
STUDY_SUMMARY
Experiments were conducted using 13-wk-old male C57BL/6J mice (Jackson Bar Harbor, ME). Mice were housed individually with free access to water and (TD.10112; Harlan Laboratories, Indianapolis, IN), with a 12:12-h light-dark and temperature and humidity control. Mice were acclimated for 1 wk prior to beginning of the experiment. The protocol was approved by the Mayo Clinic Animal Care and Use Committee. Following a 6-h fast, mice were given injections of STZ (125 mg/kg; in sodium acetate buffer, pH = 4.5) (67). were repeated on the following day. Control animals received intraperitoneal of vehicle. Only mice that displayed blood glucose ?300 mg/dl and an increase blood ketones (both values by Precision Xtra glucometer; Abbott Laboratories, Park, IL), hyperphagia, and polyuria and were positive for urine glucose via dipstick (Uristix, Bayer, Pittsburgh, PA) on day 7 after the first STZ dose included in the experiment. Animals that were positive for STZ diabetes LinBit subcutaneous insulin implant (LinShin Canada, Toronto, ON, Canada) (79) pentobarbital sodium anesthesia (Nebutal, 40 mg/kg of body wt) according to the protocol. Each animal received two subcutaneous implants (total dose: 0.2 U/24 for >30 days, 10 U/kg for 20-g mice). Insulin treatment was continued for 3 wk. animals (C; n = 13) received blank implants. Diabetic control was confirmed by measurements of blood and urinary glucose. In some cases, when urine glucose present and blood glucose was >288 mg/dl, the animal received a third implant. insulin treatment was continued until initially lower plasma glucose content in animals reached control values. Three weeks following implantation, diabetic were divided randomly into diabetic-treated (D + I; n = 13) and (D ? I; n = 13) groups. Insulin implants were removed from the D ? I group pentobarbital anesthesia, which led to the return of the diabetic phenotype 24 h. Animals from the D + I group continued on insulin treatment (Fig. 1). At age of 18 wk, animals from all groups were analyzed for body composition by an Body Composition Analyzer (EchoMRI, Houston, TX) and euthanized by decapitation wk after the initial STZ or vehicle dose. Figure 1 depicts the timeline of the and blood glucose profiles for each experimental group. Additional animals were for estimation of skeletal muscle insulin sensitivity by acute insulin The mice were divided into the C (n = 6), D ? I (n = 7), and D + I (n = 7) and followed appropriate experimental treatment, except for acute insulin 10 min prior to euthanization by pentobarbital overdose. Figure 1 of the PDF of the article summarizes the study design
Disruption of Zinc homeostasis can impair maternal glucocorticoid metabolism: on the developing fetus
STUDY_TYPE
steroid panel in pregnant rats
STUDY_SUMMARY
Steroids play a broad and vital role in regulation of gene expression, sexual characteristics, maturation, reproduction, and neurological functions; an imbalance in steroid metabolism is also linked to development and of many diseases including autism. Prenatal stress of different nature has been to affect both the mother and the offspring. Adverse nutritional conditions gestation can impair the maternal hypothalamic-pituitary-adrenal axis (HPA) and the fetus to high levels of glucocorticoids (GC). Evenwhen GC are required for brain development; an increased exposure of the fetus to GC as a consequence of stress can affect fetal hypothalamic-pituitary-gonad axis (HPG) development, neurogenesis, and have a long term impact on the offsprings mental health. zinc availability can occur during pregnancy as a consequence of different (nutritional deficiency, infections, diabetes, alcohol consumption, and to certain toxicants). Importantly, several of these gestational conditions been linked to autism. In fact, alterations in maternal zinc homeostasis upon to select environmental stressors (e.g. the phthalate plasticizer phthalate (DEHP)) that have become increasingly common since the industrial may underlie the recent rise in the incidence of autism.Alterations in maternal homeostasis could expose the fetus to high GC concentrations secondary to a maternal GC production and/or to a decreased capacity of the placenta to GC to inactive metabolites. The overall goal of this proposal is to investigate alterations in zinc homeostasis during gestation triggered by either a marginal nutrition or exposure to an environmental pollutant (the phthalate plasticizer phthalate (DEHP)) can impair maternal and fetal endocrine signaling leading to fetal brain development.
Impact of anesthesia and euthanasia on metabolomics of mammalian tissues: in a C57BL/6J mouse model
STUDY_TYPE
Anesthesia effect study
STUDY_SUMMARY
We examined the effect of several commonly-used methods of anesthesia and for collection of skeletal muscle, liver, heart, adipose and serum of C57BL/6J The data revealed tissue-specific impacts of different anesthesia and strategies. Based on these findings, we present a more optimal collection mammalian tissues and recommend that rodent tissues intended for metabolomics be collected under anesthesia rather than post-euthanasia.
INSTITUTE
University of Michigan
DEPARTMENT
Internal Medicine
LABORATORY
Evans Lab / Burant Lab
LAST_NAME
Charles
FIRST_NAME
Evans
ADDRESS
6321 Brehm Tower, 1000 Wall Street, Ann Arbor MI 48105
Monitoring In Vitro Response of Selenium-Treated Prostate Cells by 1H NMR Spectroscopy
STUDY_TYPE
Metabolite level response after treatment with organoselenium
STUDY_SUMMARY
Metabolomics analysis was performed on DU145 prostate cancer cells and PNT1A non-tumorigenic prostate cells after treatment with selenomethionine and Se-methylselenocysteine using 800 MHz Bruker NMR spectrometer on 18 cell samples.
Targeted lipids were quantified and compared to the quantities of other labs the nation. Comparisons were between pooled serum from humans who have consumed seed for the past month, pooled serums from humans who have consumed fish oil the last month, and pooled serum from humans who have not consumed either flax or fish oil for the past month. Pooled samples were prepared in triplicate.
INSTITUTE
University of Florida
DEPARTMENT
College of Medicine, Department of Pathology, Immunology, and Laboratory
Aliquots of Jurkat T-lymphocyte cells were washed with 5 different rinsing (0.3% amm. formate, 0.3% amm. acetate, 0.9% NaCl, 1 M PBS, 100 mM PBS) and ran triplicate to monitor the effect of ion suppression on the electrospray signal.
Metabolic analysis of Normal Mouse Lung Fiboblasts with/without TGFbeta treatment (Part 1)
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis (tissue/cells)
STUDY_SUMMARY
This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies, see the project for this study. This specific experiment is a small pilot study to establish method performance, it includes four biological replicas of identical cell cultures after the identical treatment and a single tissue sample.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Labeling of cells was carried out in triplicate with each unstimulated sample containing 20e6 cells and stimulated cells containing 12.8e6 cells. Cells were deprived of glucose or glutamine for 1 h then resuspended in 10mM [13C1,2] D-glucose labeled medium. At this time cells were also activated with 1 ug/ml anti-CD3 and anti-CD28. Cells were labeled (and activated) for 12 h when 1 ml of spent medium was collected and cells were resuspended in 200 ul ice cold methanol. All samples were immediately stored in -80°C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Cells were deprived of glucose or glutamine for 1 h then resuspended in 10mM [13C1,2] D-glucose labeled or 4 mM [13C5]-U-glutamine labeled medium, respectively. At this time cells were also activated with 5 ug/ml anti-CD3 and anti-CD28. Cells were labeled (and activated) for 12 h when samples were spun down, and cells were resuspended in 200 ul ice cold methanol
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Jurkat parental cells (JP6) or cells stably expressing the pCDNA Noxa vector (N5) cells were cultured to confluence and counted. 20E6 cells in triplicate were resuspended in glucose free or glutamine free medium for 2 hours. Cells were then pelleted and resuspended in 13C-1,2 Glucose (10mM) or 13C-U-glutamine (4mM) for 24 hours. Cells were pelleted and spent medium was collected. Cell pellets were washed 1X with ice cold PBS and cell pellets were resuspended in 400ul -20 methanol. Cells and media were snap frozen in liquid nitrogen and stored at -80.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
High Insulin Combined With Essential Amino Acids Stimulates Skeletal Muscle Protein Synthesis While Decreasing Insulin Sensitivity in Healthy Humans
STUDY_TYPE
High and low insulin with and without essential amino acids
STUDY_SUMMARY
Thirty participants were randomized to 3 groups of 10 each with each studied twice. Study groups comprised (1) low and high insulin, (2) low insulin and without EAAs, and (3) high insulin with and without EAAs.
Labeling of cells was carried out in triplicate with each sample containing Cells were deprived of glucose or glutamine for 1 h then resuspended in 10mM D-glucose labeled or 4 mM [13C5]-U-glutamine labeled medium, respectively. At time cells were also activated with 5 ug/ml anti-CD3 and anti-CD28. Cells were (and activated) for 16 h when samples were spun down, and cells were in 200 ul ice cold methanol. All samples were immediately stored in -80°C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The human acute lymphoblastic leukemia cell line (Jurkat) was used to isolate a clones based on Noxa expression. JP6 is low Noxa, JP3 is high Noxa. Furthermore, a Noxa expressing plasmid was tranfected and stable clones were selected for a Noxa high model (N5). 10E6 cells were starved of glucose (A) or glutamine (B&C) for 3 hours and then fed 13C 1,2 glucose (A), 15N alpha nitrogen glutamine (B) or 15N amide nitrogen glutamine (C) for 24 hours. Cells were washed 1X in ice cold PBS and resuspended in -20C methanol. Quenched cells were snap frozen and stored at -80. For experiment A we would like to observe the contribution of labeled glucose into the synthesis of amino acids, specifically glycine and serine. For experiment B we are most interested in the nitrogen incorporation into aspartate. SCB edits: This fluxomics study requires measuring amino acids for M, M+1, M+2, and M+3 prioritizing glycine, serine, aspartate, asparagine, ornithine, citrulline, then as many as possible using a diamond hydride column and LCMS method (see CEvans).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Flies were fed a normal diet or high-sugar (30% sucrose) diet for 7 days. of flies fasted for 24h or sated were microdissected and immediately frozen in ice. The microdissection process from taking the fly out of the vial to the brain took less than a minute. Each brain microdissected piece contains 50K cells.We dissected 40 brains per condition (4 conditions total) and 4-5 replicates
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
13C mass isotopomer analysis (LCMS flux studies) MLL-AF9 (part II)
STUDY_TYPE
timecourse
STUDY_SUMMARY
How cancer cells adapt to metabolically adverse conditions in patients and to proliferate is a fundamental question in cancer biology. Here we show that protein kinase (AMPK), a metabolic checkpoint kinase, confers metabolic stress to leukemia-initiating cells (LICs) and promotes leukemogenesis. Upon dietary MLL-AF9-induced murine acute myeloid leukemia (AML) activated AMPK and leukemogenic potential. AMPK deletion significantly delayed leukemogenesis and LICs by reducing the expression of glucose transporter 1 (Glut1), compromising flux, and increasing oxidative stress and DNA damage. LICs were particularly on AMPK to suppress oxidative stress in the hypoglycemic bone marrow Strikingly, AMPK inhibition synergized with physiological metabolic stress by dietary restriction and profoundly suppressed leukemogenesis. Our results that AMPK protects LICs from metabolic stress and that combining AMPK with physiological metabolic stress potently suppresses AML by inducing stress and DNA damage.
INSTITUTE
University of Michigan
DEPARTMENT
Molecular and Human genetics (Baylor College of Medicine)
Human fecal bile acid profiles before and after fecal transplant
STUDY_TYPE
Understand the bile acid profiles from the feces of fecal microbiota transplant patients that successfully recover from recurrent C. difficile infection
STUDY_SUMMARY
Understand the bile acid profiles from the feces of fecal microbiota transplant patients that successfully recover from recurrent C. difficile infection
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
U13C-Glutamine and U13C-Glucose Flux Analysis (MFA SiHa B16F10)
STUDY_TYPE
SiHa_NT and SiHa_L are 2 experimental group, control and treatment incubated with U13Cglutamine before lysis for 2 hours. SiHa_WT and SiHa_F3 are different cell isogenic clones to incubated before lysis with U13C glucose for Similarly, B1610 and B16M4 are 2 cell lines incubated before lysis with U13C for 2hours
STUDY_SUMMARY
SiHa_NT and SiHa_L are 2 experimental group, control and treatment incubated with U13Cglutamine before lysis for 2 hours. SiHa_WT and SiHa_F3 are different cell isogenic clones to incubated before lysis with U13C glucose for Similarly, B1610 and B16M4 are 2 cell lines incubated before lysis with U13C for 2hours
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
This experiment was performed using the following cohorts: 1) healthy controls, patients with scleroderma at low risk for pulmonary hypertension, 3) pateints scleroderma at high risk for pulmonary hypertension. Whole blood was drawn into stop soilution (1:1 ratio) at rest and again at peak exercise for each subject.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomic analysis of normal and diabetic mouse bone marrow under PBS or treatment
STUDY_TYPE
Untargeted Metabolomics
STUDY_SUMMARY
Wild type and diabetic (MKR) mice were treated daily with intraperitoneal of 50 microliters of PBS (control) or metformin (200 mg/kg body weight) for 14 Their bone marrow cells were collected and compared by untargeted metabolomics.
INSTITUTE
New York University
DEPARTMENT
College of Dentistry, Basic Science and Craniofacial Biology
LABORATORY
Xin Li Laboratory
LAST_NAME
Xin
FIRST_NAME
Li
ADDRESS
345 East 24th Street, Room 901D, New York, NY 10010
EMAIL
xl15@nyu.edu
PHONE
1-(212)992-7009
NUM_GROUPS
4
TOTAL_SUBJECTS
15 samples
STUDY_COMMENTS
each sample with 3 technical replicates in each mode
Sparing of muscle mass and function by passive loading in an experimental care unit model
STUDY_TYPE
time course + intervention
STUDY_SUMMARY
A unique experimental rat ICU model has been used allowing long-term (weeks) analyses of the effects of standardized unilateral passive mechanical loading skeletal muscle size and function and underlying mechanisms. Results show that mechanical loading alleviated the muscle wasting and the loss of associated with the ICU intervention, resulting in a doubling of the functional of the loaded versus the unloaded muscles after a 2-week ICU intervention.
Cardiac Resynchronization Therapy Induces Adaptive Metabolic Transitions in the Profile of Heart Failure
STUDY_TYPE
intervention
STUDY_SUMMARY
This prospective study consisted of 24 patients undergoing CRT for advanced HF 10 control patients who underwent catheter ablation for supraventricular but not CRT. Blood samples were collected before and 3 months after CRT. profiling of plasma samples was performed using gas chromatographymass and nuclear magnetic resonance.
Effect of Insulin Sensitizer Therapy on Amino Acids and Their Metabolites
STUDY_TYPE
drug + time course
STUDY_SUMMARY
We previously reported the overall study design for the parent study [29]. The report primarily examines the effect of three months of insulin sensitizer on plasma concentrations of BCAA, AAA, and AA metabolites in overweight/obese with fasting hyperglycemia, defined as either impaired fasting glucose or diabetes [29]. Briefly, 25 drug naïve, Northern European American participants fasting blood glucose concentrations of 108?180 mg/dL were randomized to either 45 mg of pioglitazone per day plus 1 g of metformin twice per day (n = or placebo (n = 13) for 12 weeks. We chose metformin based on its proven effect hepatic insulin sensitivity and pioglitazone based on its effect on peripheral sensitivity. Current use of hypoglycemic medications excluded participants from present study.
In this experiment 2 day old baby mice were exposed to hyperoxia (75% O2) for 14 days. Control baby mice were housed in room air (normoxia). Plasma and lavage fluid (BALF) were harvested after 14 days of exposure (on Day of life
STUDY_SUMMARY
In this experiment 2 day old baby mice were exposed to hyperoxia (75% O2) for 14 days. Control baby mice were housed in room air (normoxia). Plasma and lavage fluid (BALF) were harvested after 14 days of exposure (on Day of life
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
13C mass isotopomer analysis (LCMS flux studies) MLL-AF9 (part III)
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis (tissue/cells)
STUDY_SUMMARY
How cancer cells adapt to metabolically adverse conditions in patients and to proliferate is a fundamental question in cancer biology. Here we show that protein kinase (AMPK), a metabolic checkpoint kinase, confers metabolic stress to leukemia-initiating cells (LICs) and promotes leukemogenesis. Upon dietary MLL-AF9-induced murine acute myeloid leukemia (AML) activated AMPK and leukemogenic potential. AMPK deletion significantly delayed leukemogenesis and LICs by reducing the expression of glucose transporter 1 (Glut1), compromising flux, and increasing oxidative stress and DNA damage. LICs were particularly on AMPK to suppress oxidative stress in the hypoglycemic bone marrow Strikingly, AMPK inhibition synergized with physiological metabolic stress by dietary restriction and profoundly suppressed leukemogenesis. Our results that AMPK protects LICs from metabolic stress and that combining AMPK with physiological metabolic stress potently suppresses AML by inducing stress and DNA damage.
INSTITUTE
University of Michigan
DEPARTMENT
Molecular and Human genetics (Baylor College of Medicine)
THP-1 Human Monocyte cells (10^6) were seeded in RPMI 1640 with 0.5% FBS. The were incubated for 30 minutes in either no citrate, 1 mM citrate, or 6 mM Separately, cells were either incubated in 1 mM 13C6 citrate or 6mM 13C6 (Sigma-Aldrich #606081). After the 30 minute pre-incubation time, the cells harvested or stimulated with lipopolysaccharide (LPS) for 1 h or 30 min. Cells subsequently spun down and washed in 150mM ammonium acetate. Cell were respun the supernatant was discarded. Cells were flash frozen in liquid nitrogen and on dry ice.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Comparative metabolomics study of WT and iButOH tolerant E. coli
STUDY_SUMMARY
This study aims to elucidate metabolic mechanisms of tolerance to isobutanol in coli. Two strains are utilized: WT parental strain EcHW24, and isobutanol strain 38-20-4 created via multiplex genome engineering. The metabolic response growth with isobutanol (0.7% w/v) and without (0% w/v) on NG50 minimal media be compared for each strain. 3 replicates for each strain/iButOH concentration been submitted, excpet for WT/0.7%; we have observed high growth phenotype for this combination, and have corresponding submitted 5x replicates. Strain contains mutations in the TCA cycle (gltA SNP) and amino acid metabolism indels in glnE, gltD, and tnaA), thus our hypothesis is that tolerance arises rewiring of TCA cycle and amino acid metabolism, possibly resulting in intracellular ratio of glutamine:glutamate
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The experiment was done on 4/2/2014 and consists of 7 experimental conditions x replicates per condition = 14 samples. The experimental duplicates are numbered (i.e. 1 and 2, 3 and 4, etc.). All samples are primary mouse macrophages from bone marrow. 12 million cells were plated in each 10 cm tissue culture plate (Corning) and the following day the cells were stimulated with LPS, CL097 and/or Gardiquimod in 10 mls of 2% FBS 25 mM HEPES IMDM. After 60 minutes medium was aspirated and the cells were rapidly wahsed with 15 mls of 150 mM acetate and after aspiration liquid nitrogen was poured on top of the cells and to -80 C freezer. Sample pairs 7 - 8 and 9-10 were treated identically except the rinse was done with ammonium acetate (7 and 8) or distilled water (9 and to evaluate the effect of the rinse solution in the quality of the obtained
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
T cell metabolism during graft-versus-host disease (CAB 307)-PART I
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis (tissue/cells)
STUDY_SUMMARY
T cells were injected into mice to model graft-versus-host disease. On day 7 after bone marrow transplantation (BMT), cells were recovered and CD8 T cells were purified to > 90% purity over magnetic columns. Naïve T cells were used as control. Cells were then plated at 5x10^6 cells/ml onto plates coated with anti-CD3/CD28 antibodies in the presence of 300µM 13C-palmitate conjugated to BSA (in PBS). Cells were incubated at 37oC for 60min, after which time they were removed from the plates, counted, and an equal number (2.5x10^6) were placed into a 1.7 ml micro-centrifuge tubes and spun down. Cells were washed once with ammonium chloride, residual volume was removed by a second brief spin, cell pellets were flash frozen in liquid nitrogen and stored at -80oC until analysis. Several mice lines were used in this study.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We recently reported superior right ventricle (RV) performance in response to acute afterload challenge in lambs with a model of congenital heart disease with chronic left-to-right cardiac shunts. Compared with control animals, shunt lambs demonstrated increased contractility because of an enhanced Anrep effect (the slow increase in contractility following myocyte stretch). This advantageous physiological response may reflect preservation of a fetal phenotype, since the RV of shunt lambs remains exposed to increased pressure postnatally. Nitric oxide (NO) production by NO synthase (NOS) is activated by myocyte stretch and is a necessary intermediary of the Anrep response. The purpose of this study was to test the hypothesis that NO signaling is increased in the RV of fetal lambs compared with controls and shunt lambs have persistence of this fetal pattern. An 8-mm graft was placed between the pulmonary artery and aorta in fetal lambs (shunt). NOS isoform expression, activity, and association with activating cofactors were determined in fetal tissue obtained during late-gestation and in 4-wk-old juvenile shunt and control lambs. We demonstrated increased RNA and protein expression of NOS isoforms and increased total NOS activity in the RV of both shunt and fetal lambs compared with control. We also found increased NOS activation and association with cofactors in shunt and fetal RV compared with control. These data demonstrate preserved fetal NOS phenotype and NO signaling in shunt RV, which may partially explain the mechanism underlying the adaptive response to increased afterload seen in the RV of shunt lambs. Research is published, core data not used but project description is relevant: http://ajpheart.physiology.org/content/309/1/H157.long
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
This experiment was performed in wild type vs. CD39 knockout (KO) mice that had infusions of either saline or apyrase over the course of 2 weeks. Whole blood obtained via intracardiac puncture, and was drawn into a syringe prefilled with anti-enzyme stop solution.
STUDY_SUMMARY
This experiment was performed in wild type vs. CD39 knockout (KO) mice that had infusions of either saline or apyrase over the course of 2 weeks. Whole blood obtained via intracardiac puncture, and was drawn into a syringe prefilled with anti-enzyme stop solution.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Patients between age of 6 weeks and 16 years of age who were undergoing small resection were selected, including those who were either receiving enteral preoperatively (control group), or those who were without enteral nutrition and TPN (TPN group). At the time of operation, 100-500 microliters of effluent from small bowel lumen was aspirated during the small bowel resection. The samples immediately frozen in liquid nitrogen and stored at -80deg. After five control five TPN samples were collected, all samples were submitted for amino acid to quantify the relative amounts of amino acids in the small bowel effluent each patient. We hypothesize that the TPN group will contain higher levels of amino acids present in TPN, such as leucine, phenylalanine, and valine.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Samples 4-34 are sera and feces from an experiment to determine the effects of on SCFA in Ang II-induced hypertension. Samples 35-59 are plasma samples fron experiment to determine the effects of ACE2 activator, DIZE on SCFA in pulmonary hypertension. Plasma samples were collected using heparin
STUDY_SUMMARY
Samples 4-34 are sera and feces from an experiment to determine the effects of on SCFA in Ang II-induced hypertension. Samples 35-59 are plasma samples fron experiment to determine the effects of ACE2 activator, DIZE on SCFA in pulmonary hypertension. Plasma samples were collected using heparin
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
This is a time restricted feeding study (see M Hatori, et al. Cell Metabolism 15(6), 848-860)
STUDY_SUMMARY
This is a time restricted feeding study (see M Hatori, et al. Cell Metabolism 15(6), 848-860). Briefly, there are four groups of mice: (1) NA mice are on a chow ad libitum diet; (2) FA mice are on a high fat ad libitum diet (i.e. Diet obesity); (3) FT mice are on a high fat time restricted diet (i.e. only eat for hours/day and fast for 16); and (4) CDKO mice which are cry knock out mice on a chow ad libitum diet. We have collected stool from these four groups while they in the light and in the dark. Our expectation is that their stool metabolites be different at different times of the day.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Twelve weeks old WT and BAF60a Liver specfific knockout mice were fed with high diet for 8 weeks. Mice were sacrified after 4 h of starvation. Blood samples harvested by heart puncture for plasma. Liver were dissected and immediately in liquid nitrogen. All the samples were kept in -80oC freezer for long term
STUDY_SUMMARY
Twelve weeks old WT and BAF60a Liver specfific knockout mice were fed with high diet for 8 weeks. Mice were sacrified after 4 h of starvation. Blood samples harvested by heart puncture for plasma. Liver were dissected and immediately in liquid nitrogen. All the samples were kept in -80oC freezer for long term
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Lanthanide-mineral induced alteration of bile acid metabolism in a murine model steatohepatitis
STUDY_SUMMARY
120 mice (equal number of males and females) were randomized into 3 equal One group is on a HFWD alone, a second group is on HFWD supplemented with and calcium, and a third control group is supplemented with calcium alone. At termination (18 months) we will harvest hepatocytes and colonic enterocytes for of epithelial gene expression patterns. We will also harvest cecal contents and for microbial profiling by 16S rRNA pyrosequencing. For this small pilot we wish to add an untargeted metabolomic analysis component. We will harvest (right medial lobe with gall bladder), serum, and feces. We will assay liver/gall bladder samples (8 from the HFWD group and 8 from the supplemented group). Remaining liver samples and the serum and feces will be for future investigation. Liver is being targeted first since both and hepatocellular carcinoma were seen in our previous study in mice on HFWD Additionally, alterations of bile acid profiles and bile acid metabolism have associated with both steatohepatitis and hepatic cancers.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Understand the differences in Bile Acid composition between knockout and floxed at each intestinal segment. Also difference in metabolites between these two at each level of the intestine.
STUDY_SUMMARY
Understand the differences in Bile Acid composition between knockout and floxed at each intestinal segment. Also difference in metabolites between these two at each level of the intestine.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Murine gastrointestinal bile acid profiles before and after antibiotics
STUDY_SUMMARY
Mice were treated with cefoperazone for 10 days and then allowed 6 weeks to off of the antibiotic. Other antibiotic treatments included IP clindamycin the 6 week recovery, IP clindamycin alone, vancomycin alone, kanamycin alone metronidazole. Gut luminal contents of these mice were collected at the time of and included both ileal and cecal content. Paired samples will be used for both analysis and targeted bile acid analysis to define how gut bacteria alter bile profiles in the gut and in turn how this affects C. difficle spore germination outgrowth.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Liver and Plasma metaboites for 13C-glucose load in wild type, LIRKO and LIRFKO
STUDY_SUMMARY
Mice were fasted for 18 hr overnight then sacrificed or treated with (2 g/kg ip) and sacrificed 1 hr later by decapitation and liver was immediately and stored in liquid N2 and then at -80 C. Wild type (IR and IR/FoxO1 floxed) were sacrificed after fasting and 1 hr post-glucose treatment. Liver-specific receptor knockout (LIRKO) and insulin receptor/FoxO1 double knockout (LIRFKO) were sacrificed 1 hr post glucose treatment
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Tumor neurospheres were grown in culture until 90% confluent. To collect cells, were filtered through 0.45um nylon filters (Fischer Sci 099029) that were with methanol and ultrapure water using a microanalytical glass filter holder Sci 09753E). The cells were filtered through filtration apparatus, then washed 1mL of distilled water very quickly. Filter paper is taken immediatedly with and plunged cell side down into 6-well plate filled with liquid nitrogen placed dry ice. Plate is wrapped in aluminum foil and stored at -80C before the liquid evaporates. Samples are shipped on dry ice
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
THP-1 Human Monocyte cells (10^6) were seeded in RPMI 1640 with 0.5% FBS. The were incubated for 30 minutes in either no citrate, 1 mM citrate, or 6 mM Separately, cells were either incubated in 1 mM 13C6 citrate or 6mM 13C6 (Sigma-Aldrich #606081). After the 30 minute pre-incubation time, the cells harvested or stimulated with lipopolysaccharide (LPS) for 1 h or 30 min. Cells subsequently spun down and washed in 150mM ammonium acetate. Cell were respun the supernatant was discarded. Cells were flash frozen in liquid nitrogen and on dry ice.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Wild type and AMPK KO bone marrow derived macrophage were stimulated with LPS for various time period and plates were frozen in liquid nitrogen after washing sodium acetate (200uM) solution and kept in deep freezer for further analysis.
STUDY_SUMMARY
Wild type and AMPK KO bone marrow derived macrophage were stimulated with LPS for various time period and plates were frozen in liquid nitrogen after washing sodium acetate (200uM) solution and kept in deep freezer for further analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
T cell metabolism during graft-versus-host disease (CAB 307)-PART II
STUDY_SUMMARY
T cells were injected into mis-matched animals undergoing bone marrow On day 7 after BMT, cells were receovered and CD8 T cells were purified to > purity over magnetic column. Cells were washed once in PBS, then once in chloride, residual volume was removed and cell pellets were flash frozein in and stored at -80C
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Changes to bile acids in the murine gut after antibiotics
STUDY_SUMMARY
Changes to bile acids in the murine gut after antibiotics
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@umich.edu
PHONE
-
NUM_GROUPS
12
TOTAL_SUBJECTS
60
STUDY_COMMENTS
Samples were collected at the time of necropsy. Contents from the lumen of the tract of C57BL/6 mice were collected, flash frozen and stored in the -80C until for metabolomics assay. C57BL/6 mice treated with cefoperazone for 5 days with days of water (n=5) were harvested along with non-antibiotic treated mice Contents from the small intesine (duodenum, jejunum and ileum), the large (cecum, colon) and stool were collected for targeted bile acid analysis.
Liver and Plasma metaboites for 13C-glucose load in wild type, LIRKO GTT 1 mice
STUDY_TYPE
13C mass isotopomer analysis (flux studies)
STUDY_SUMMARY
Mice were fasted for 18 hr overnight then sacrificed or treated with 13C-U-glucose (2 g/kg ip) and sacrificed 1 hr later by decapitation and liver was immediately freeze-clamped and stored in liquid N2 and then at -80 C. Wild type (IR and IR/FoxO1 floxed) mice were sacrificed after fasting and 1 hr post-glucose treatment. Liver-specific insulin receptor knockout (LIRKO) and insulin receptor/FoxO1 double knockout (LIRFKO) mice were sacrificed 1 hr post glucose treatment. http://www.nature.com/ncomms/2015/150512/ncomms8079/full/ncomms8079.html
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Role of Microbiome in Psoriatic Arthritis (SCFA in PsA)
STUDY_SUMMARY
To investigate associations of gut and skin microbiota diversity with psoriatic pathogenesis.Characterize the abundance and diversity of gut microbiota in with never-treated, new-onset psoriatic arthritis (PsA). Methods: 16s rRNA pyrosequencing was utilized to compare the community composition of microbiota in PsA patients, psoriasis patients and healthy, matched controls. from patients with PsA, psoriasis of the skin (Ps), new-onset rheumatoid (NORA) and healthy controls were assessed for the presence and levels of fecal immunoglobulin A (sIgA) and various proteins and pro-inflammatory cytokines
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Comparison of normal, lung adenocarcinoma and SCLC tissue metabolomes
STUDY_SUMMARY
In addition to the generation and analysis of metabolomics data on cell lines, of normal lung tissue, adenocarcinoma lung tissue and small cell lung carcinoma (seven samples/group) were processed and evaluated metabolite profile under the scope of the pilot and feasibility study. These data can be to the metabolite profiles defined in the SCLC and NSCLC cell lines and with the ABPP-determined metabolic kinases to identify distinct metabolic or biomarkers (?oncometabolites?) that distinguish small cell lung cancer from cell lung cancer.
Normal plasma cells,Low proliferation multiple myeloma and High proliferation myeloma cells
STUDY_TYPE
differential metabolomics
STUDY_SUMMARY
CD138 sorted bone marrow plasma cell were obtained from a normal patient, a myelow with slow proliferation and a multiple myelow with rapid proliferation.
Bile acid targeted metabolomics of the small intestine in malnourished and mice
STUDY_TYPE
Targeted metabolomics
STUDY_SUMMARY
A total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks a malnourished diet or a control-fed isocaloric diet. Samples were taken from small intestinal fecal content at the terminus of the ileum for targeted bile analysis.
INSTITUTE
University of Victoria
DEPARTMENT
The Uvic Proteomics and Metabolomics Innovation Centre
LAST_NAME
Borchers
FIRST_NAME
Christoph
ADDRESS
#3101-4464 Markham St Victoria, BC Canada, V8Z 7X8
EMAIL
christoph@proteincentre.com
PHONE
-
NUM_GROUPS
2
TOTAL_SUBJECTS
8*
STUDY_COMMENTS
*One sample failed quality control in the malnourished group, thus was not in the study
1) Characterize plasma metabolome in Barth Syndrome 2) To implement targeted, quantitative studies on prospective biomarkers and metabolites of interest derived from the non-targeted phase.
Vitamin targeted metabolomics of the small intestine in malnourished and mice
STUDY_TYPE
Targeted metabolomics
STUDY_SUMMARY
A total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks a malnourished diet or a control-fed isocaloric diet. Samples were taken from small intestinal fecal content at the terminus of the ileum for targeted of vitamin concentrations.
INSTITUTE
University of Victoria
DEPARTMENT
The Uvic Proteomics and Metabolomics Innovation Centre
LAST_NAME
Borchers
FIRST_NAME
Christoph
ADDRESS
#3101-4464 Markham St Victoria, BC Canada, V8Z 7X8
Metabolomics Reveals that Aryl Hydrocarbon Receptor Activation by Environmental Chemicals Induces Systemic Metabolic Dysfunction in Mice (Part I)
STUDY_TYPE
drug dosage
STUDY_SUMMARY
12 mice were acclimatized for a week, taught to eat dough pills then half were treated with TCDF per pill per day for 5 days Also 10 AHR -/- mice were used and treated the same way
Concentrations of cocaine (5,3,2,1.5,1,0.75,0.5,0.25,0.125, 0.062, and 0.031 were spiked into whole human blood for MALDI-MS analysis. A 10 uL volume of mixture was allowed to dry on Whatman Grade 2 filter paper. A 1ppm Cocaine-d3 was used as an internal standard. Parameters of the MALDI system optimized, including laser energy, number of laser shots, and matrix. The standard was added on top of the dried blood spot sample. Wide isolation tandem was used to generate a calibration curve.
INSTITUTE
University of Florida
DEPARTMENT
Chemistry
LABORATORY
Chemistry Lab Building
LAST_NAME
Dhummakupt
FIRST_NAME
Elizabeth
ADDRESS
R3-226 Academic Research Building, Department of Biochemistry and Molecular PO Box 100245, Gainesville, FL 32610-0245
EMAIL
emuffly@ufl.edu
PHONE
352-392-0515
NUM_GROUPS
11
TOTAL_SUBJECTS
154
STUDY_COMMENTS
11 concentrations were run as 7 samples/concentration for 2 days
Analysis of Dried Blood Spots by Paper Spray Ionization - MS
STUDY_TYPE
Analysis of Dried Blood Spots by Paper Spray Ionization - MS
STUDY_SUMMARY
Concentrations of cocaine (6, 5,3,2,1.5,1,0.75,0.5,0.25,0.125, 0.062, and 0.031 were spiked into whole human blood for PS-MS analysis. A 10 uL volume of mixture was allowed to dry on Whatman Grade 2 filter paper. A 1ppm Cocaine-d3 was used as an internal standard. Parameters of the paper spray were optimized, including spray voltage, capillary temperature and solvent. The standard was added on top of the dried blood spot sample. Wide isolation tandem was used to generate a calibration curve.
INSTITUTE
University of Florida
DEPARTMENT
Chemistry
LABORATORY
Chemistry Lab Building
LAST_NAME
Dhummakupt
FIRST_NAME
Elizabeth
ADDRESS
R3-226 Academic Research Building, Department of Biochemistry and Molecular PO Box 100245, Gainesville, FL 32610-0245
EMAIL
emuffly@ufl.edu
PHONE
352-392-0515
NUM_GROUPS
11
TOTAL_SUBJECTS
154
STUDY_COMMENTS
11 concentrations were run as 7 samples/concentration for 2 days
Untargeted metabolomic analysis of the small intestinal content of malnourished
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
A total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks a malnourished diet or a control-fed isocaloric diet. Samples were taken from small intestinal fecal content at the terminus of the ileum.
INSTITUTE
University of Victoria
DEPARTMENT
The Uvic Proteomics and Metabolomics Innovation Centre
LAST_NAME
Borchers
FIRST_NAME
Christoph
ADDRESS
#3101-4464 Markham St Victoria, BC Canada, V8Z 7X8
Metabolomics Reveals that Aryl Hydrocarbon Receptor Activation by Environmental Induces Systemic Metabolic Dysfunction in Mice (Part II)
STUDY_TYPE
Time course
STUDY_SUMMARY
12 C57BL/6J male mice were acclimatized for 1 week and then divided into two and trained to eat dough pills. One group was control and the other was exposed TCDF through the dough pills. The mice were treated for 5 days at a dosage of TCDF for a final concentration of 5μg/kg body weight. Also looked at were mice and they were treated the same way as the C57BL/6J mice.
INSTITUTE
Pennsylvania State University
DEPARTMENT
Department of Veterinary and Biomedical Sciences
LAST_NAME
Patterson
FIRST_NAME
Andrew
ADDRESS
101 Life Sciences, University Park, State college, 16802
Adult (14 weeks old) Sprague-Dawley rats showing at least three consecutive periods (4 day) of estrous cycles were randomly assigned to four groups: 1: 2: nicotine (6 mg/kg), 3: OC and 4: nicotine (6 mg/kg) + OC. Rats were exposed these treatments for a month. At the end of treatments, hippocampus was immediately frozen in liquid nitrogen. We are sending one side of hippocampi to Center for Integrated Metabolomics for analysis at the University of Florida.
Quick Comparison of Urine Metabolites in Human and SD Rats of Different Sex by UPLC-TOFMS and In-house Software Platform
STUDY_TYPE
Biomarker Discovery
STUDY_SUMMARY
Human urine samples were collected before breakfast from 14 male and 13 female post-graduate students, age from 23 to 29, on the morning of sample collection Male (n=8) and female (n=8) SD rats weighing between 220 and 250g were used. On morning of sample collection day, each rat was deprived of food and put in cage for 24h urine collection. All urine samples were frozen at -80°C prior to
Quick Comparison of Serum Metabolites in SD Rats of Different Sex by Untargeted and In-house Software Platform
STUDY_TYPE
Biomarker Discovery
STUDY_SUMMARY
Male (n=8) and female (n=8) SD rats weighing between 220 and 250g were used. On morning of sample collection day, each rat was deprived of food and put in cage for 24h urine collection. Then a blood sample (3-5ml) was collected from aorta of the rat under anesthesia and centrifuged to obtain serum. All urine serum samples were frozen at -80°C prior to analysis.
Sexual antagonism in exuded non-volatile metabolites in C. purpureus
STUDY_TYPE
male - female
STUDY_SUMMARY
The experimental approach seeks to test for sexual dimorphism in exuded metabolites in C. purpureus. The proposed research is creative and original in its inter-disciplinary approach and its use of a biochemically tractable to develop a much-needed link between natural selection for sexual dimorphism the molecular targets of that selection pressure.
Cyclobutene- and cyclobutane-functionalized fatty acids as novel biochemical of structure and function in HepG2 cells
STUDY_TYPE
Lipid analysis novel C18 fatty acid anologues in complex lipids
STUDY_SUMMARY
Human hepatoma HepG2 cells (American Type Culture Collection; HB-8065) were in 75 ml tissue cell culture flasks in Eagle's minimal essential medium (EMEM) with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO2. treatment with fatty acids or analogues, the cells were seeded at a density of × 106 cells in a T25-cm2 flask for 24 h. Each FA or analogue was added to the medium as a fatty acid-bovine serum albumin (BSA) complex (2.5:1, FA:BSA) to the desired final concentration. The controls in these experiments were HepG2 with BSA alone. After 24 h treatment, the media was collected, cells were twice with PBS and cells were harvested for analysis. To each cell suspension to lipid extraction a standard mixture of 25 µg C15:0 PE, C17:0 PC and C71:1 was added as standards. Extraction of lipids was performed according to the method. For metabolomics analysis, the lipid extracts were resuspended in 2:1 (v/v).All analyses were carried out using an Agilent 1200 Series HPLC, ACE C8-300 column (2.1 x 100 mm) and linear gradient elution at a flow rate of 0.1 Mobile phase A and B consisted of 0.1% formic acid; 10 mM ammonium acetate in and 0.1% formic acid; 10 mM ammonium acetate in ACN/isopropanol (50/50; v/v), The injection volume was 4 µL. Separation of metabolites was achieved at the gradient: T=0 min: 30% B; T=1 min: 30% B; T=25 min: 100% B; T=45 min: 100% B; min: 30% B; and T=60 min: 30% B (re-equilibration). The HPLC system was coupled to a Bruker Soalrix 70 Hybrid FTMS instrument equipped with ionization source (ESI) (Bruker Daltonics). The system was controlled by HyStar software. MS data was collected with resolving power of 78,000 (at m/z 400) in or negative mode under following conditions: a capillary voltage of (+/-) 4,500 and an end plate offset of -500 V. The dry temperature was set at 180°C. Dry flow was maintained 4 L/min. Acquisition range was 244-1,800 m/z with 0.2 s ion time. LC-MS data was converted into mzXML format using CompassXport v. 3.0.6 processed by mzMine v.2.10 [25] or XCMS data analysis software. Data processing mass detection, chromatographic peak detection and deconvolution, isotopic grouping, normalization and peak alignment. Metabolite data were mean-centered unit-variance scaled to remove the offsets and adjust the importance of high low abundance metabolites to an equal level. Significantly altered metabolites defined by a fold change (FC) >2 and p<0.05. Principal component analysis (PCA) hierarchical clustering analysis (HCA) of signature metabolites altered in treated cells compared to control were performed in the Metaboanalyst web (www.metaboanalyst.ca).
INSTITUTE
University of Nebraska - Lincoln
DEPARTMENT
Biochemistry
LABORATORY
DiRusso Black FATTT Lab
LAST_NAME
DiRusso
FIRST_NAME
Concetta
ADDRESS
Department of Biochemistry, University of Nebraska-Lincoln, N241 Beadle Center Vine St.
EMAIL
cdirusso2@unl.edu
PHONE
402-472-6504 or 402-613-9293
NUM_GROUPS
8
TOTAL_SUBJECTS
24+24=48
STUDY_COMMENTS
8 groups in triplicate ran in both negative and positive mode
Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole medium
STUDY_TYPE
differential metabolomics
STUDY_SUMMARY
Media was flash frozen with N2 and stored at -80 C. Samples can be stored at C until use. ~1 ml aliquots. The following media has been provided to the core in biological triplicates.Complete (Whole) Media:1) Whole unconditioned (Defined culture media, M199)2) Whole M1 medium3) Whole M2 medium
Metabolomic-based investigation on the effects of antifungal agents in Candida
STUDY_TYPE
in vitro study/drug dosage
STUDY_SUMMARY
Our aim is to determine the metabolic effects of increasing doses of an agent on C. albicans metabolism (untargeted, steady state metabolomics). We culture in vitro Candida cells to the mid-logarithmic growth in liquid media at 37°C and then inoculate biological replicates (1ml) onto 22mm filters under vocuum filtration in sterile conditions. Subsequently, isolates be cultivated to midlogarithmic phase of growth on the same agar (RPMI-1640) to the antifungal agent has been added at a range of concentrations to achieve equivalent to 0 MIC (no drug), 0.0625 MIC, 0.125 MIC, 0.25 MIC, 0.5 MIC and 1.0 at 37°C. At mid-logarithmic phase of growth (12h) replicates will be quenched by immersion into a solvent mixture of 40% acetonitrile: 40% methanol: water precooled at -40°C. The resulting quenched isolate/solvent mixtrue will mechanically lysed by bead-beating with 0.1mm Zirconia beads in a tissue and then centrifuged to seperate out cell wall components. Supernatants will be and stored at -80°C until they will be sent to SECIM facility.
In this project we will investigate the feasibility of metabolomics and to the diversity of ?metabotypes? in the horse, towards discovery of markers and associated with obesity and insulin resistance in the equine model. The team of researchers assembled for this work have identified horses severely with Equine Metabolic syndrome, often characterized by obesity and These animals are all from the Arabian breed, to control for some genetic Horses are age, sex and farm of residence matched with a control animal possible. Carefully controlled collection protocols were utilized to ensure variability in sample age and quality. Blood plasma is submitted for both LC-MS analysis through the SECIM core facilities. This discovery-based approach begin to generate new targets for the development of novel therapeutic for the treatment and prevention of obesity, type-2 diabetes as well as related conditions in both humans and horses. Finally, as the first dataset of its kind the horse, we may also be able to highlight promising new biomarkers for diagnostic use.
Aliquots of Jurkat T-lymphocyte cells were extracted using the Folch or Matyash at different total volumes and run in triplicate to calculate the extraction for each method.
INSTITUTE
University of Florida
DEPARTMENT
Dept. of Chemistry/SECIM
LABORATORY
Biomedical Mass Spectrometry Lab
LAST_NAME
Ulmer
FIRST_NAME
Candice
ADDRESS
R3-226 Academic Research Building, Department of Biochemistry and Molecular PO Box 100245, Gainesville, FL 32610-0245
Determining the metabolic profile of wildtype and nos mutant Staphylococcus grown in media lacking glucose using targeted LC/MS
STUDY_TYPE
Single time point
STUDY_SUMMARY
Whole cells from wildtype, nos mutant, SrrAB mutant, SrrAB nos double mutant, complement strains will be isolated for targeted metabolite analysis. In supernatants (extracellular metabolites) will also be analyzed for their profile.
Measurement of free amino acid (AA) in response to MYC
STUDY_TYPE
treatment
STUDY_SUMMARY
The proposed study will provide us information how the different AAs are by MYC. MYC is known to cause increased levels of glutamin due to import and but we hypothesize that the overall pool of free AA in the cells is reduced, when cells are starved.
Impact of recurrent hypoglycemia on brain metabolite profile
STUDY_TYPE
Insulin treatment in diabetic rats
STUDY_SUMMARY
The goal of this study is to determine the effect of mild / moderate on brain metabolism. To achieve this goal insulin-treated diabetic rats will be to recurrent mild / moderate hypoglycemia.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Dave
FIRST_NAME
Kunjan
ADDRESS
-
EMAIL
Kdave@med.miami.edu
PHONE
305-243-3590
NUM_GROUPS
2
TOTAL_SUBJECTS
40
STUDY_COMMENTS
Two groups (i) Insulin treated diabetic + Recurrent hypoglycemia, (ii) Insulin diabetic + Recurrent hypoglycemia (only insulin injection) + Glucose infusion maintain glucose to baseline levels.Total 40 samples. Description: Ten samples and 10 hypothalamus sample from ITD+RH group of rats.Similarly, Ten samples and 10 hypothalamus sample from ITD+RH+Glucose group of rats.
NIH WCMC Pilot & Feasibility Project: Metabolomics of Neonatal Pulmonary
STUDY_TYPE
Treatment and feeding study
STUDY_SUMMARY
Targeted metabolomic analyses of oxylipins were performed on 16 rat plasma and samples collected from rats euthanized at 14 days following exposure to growth and/or hyperoxia. Samples were analyzed by UPLC-MS/MS using a Waters Acquity and detected on an API 4000 QTrap (AB Sciex, Framingham, MA, USA) by multiple monitoring (MRM) after negative mode electrospray ionization.
The role of microbial metabolites in experimental liver disease
STUDY_TYPE
Targeted Metabolomic Analysis of plasma samples
STUDY_SUMMARY
Aim 1: Our experimental approach is to understand the effect of drinking water bacterial metabolite, Indole-3-propionic Acid (IPA), in liver disease in an alcohol model. Aim 2: Determine the levels of IPA in plasma of conventional in a chronic alcohol model.Aim 3: Determine the levels of IPA in plasma of WT (C57BL/6) and mutant SL (sublytic, which is a mouse with a point mutation in mice.
NIH WCMC Pilot & Feasibility Project: Metabolomics of Neonatal Pulmonary in human
STUDY_TYPE
Case-control study
STUDY_SUMMARY
Targeted metabolomic analyses of oxylipins were performed on 40 human umbilical plasma samples collected from infants born prematurely (gestational age <37 Samples were analyzed by UPLC-MS/MS using a Waters Acquity UPLC and detected on API 4000 QTrap (AB Sciex, Framingham, MA, USA) by multiple reaction monitoring after negative mode electrospray ionization.
NIH WCMC Pilot & Feasibility Project: Metabolite changes associated with loss
STUDY_TYPE
Feeding study
STUDY_SUMMARY
Targeted metabolomic analyses of oxylipins, endocannabinoids, and ceramides performed on 18 mouse liver, adipose, hypothalamus, plasma, and muscle samples from mice euthanized at 18 weeks following consumption of three diet regimens induced lean, obese, and weight loss phenotypes. Samples were analyzed by using a Waters Acquity UPLC and detected on an API 4000 QTrap (AB Sciex, MA, USA) by multiple reaction monitoring (MRM) after negative mode electrospray
Metabolic contribution of pSymA and pSymB megaplasmid/chromid for multipartite Sinorhizobium meliloti cultured in minimal M9 medium
STUDY_TYPE
megaplasmid deletion
STUDY_SUMMARY
To understand the contribution of pSymA and pSymB to the metabolism of S. meliloti, the intracellular metabolome was analyzed at five time points (exponential and stationary growth phases) across the growth curve of strains with or without pSymA and/or pSymB grown in a defined, minimal medium (M9).
INSTITUTE
McMaster University
DEPARTMENT
Department of Biology
LAST_NAME
Finan
FIRST_NAME
Turlough
ADDRESS
Department of Biology, McMaster University, Hamilton, Canada L8S4K1
metabolic contriubtion of pSymA and pSymB megaplasmid/chromid for multipartite meliloti cultured in rich LBmc medium
STUDY_TYPE
megaplasmid deletion
STUDY_SUMMARY
We wished to evaluate the contribution of pSymA and pSymB towards the of various metabolites in a nutritionally complex environment and to examine S. meliloti influences its surrounding environment.
INSTITUTE
McMaster University
DEPARTMENT
Department of Biology
LAST_NAME
Finan
FIRST_NAME
Turlough
ADDRESS
Department of Biology, McMaster University, Hamilton, Canada L8S4K1
We analyzed metabolites in the brains of wild type mice and DJ-1 knockout mice. The DJ-1 knockout mouse is a model of an inherited form of Parkinson's disease.
INSTITUTE
National Institute on Aging
DEPARTMENT
Laboratory of Neurogenetics
LABORATORY
Cell Biology and Gene Expression Section
LAST_NAME
Hauser
FIRST_NAME
David
ADDRESS
35 Lincoln Drive, BLDG 35, Room 1A-1012, Bethesda, MD 20892
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1713
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints X with/without GTP
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1016
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3280
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3244
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3801
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3722c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3311
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Mice were fed with a TFD for 8 or 24 weeks to induce NAFLD or NASH, Targeted analyses examined diacylglycerols and ceramides in 6-8 mice per group 4 groups including 8 week control, 24 week control, 8 week TFD, and 24 week Samples were analyzed via UHPLC-HRMS
INSTITUTE
University of Florida
DEPARTMENT
Chemistry
LABORATORY
Yost Laboratory
LAST_NAME
Patterson
FIRST_NAME
Rainey
ADDRESS
214 Leigh Hall, University of Florida, Gainesville, FL 32611
Serum samples from Mla patients responsive or not responsive to chemotherapy
STUDY_SUMMARY
In the current study we will perform global metabolic profiling on serum obtained at diagnosis from pediatric AML patients (n=20) treated under St. Jude clinical trial to identify potential biomarkers of clinical significance. These include 10 responders and 10 non responders. In a subset of patients (n=7), we matched samples that were obtained at remission allowing us to determine the in serum metabolome at diagnosis and after remission followed by investigation the metabolome change analysis with clinical response.
Pyruvate isotopically labeled by 13C either at position 1 or 2 was used to carbon flux in 3T3-L1 mouse cells line in the presence of various combinations drugs
INSTITUTE
University of Michigan
DEPARTMENT
Molecular and Integrative Physiology (MCTP)
LABORATORY
Macdougald Lab (MCTP)
LAST_NAME
MacDougald
FIRST_NAME
Ormond
ADDRESS
University Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105
To understand the contribution of adipose tissue fatty acid oxidation to metabolism, we generated mice with an adipose-specific knockout of carnitine 2 (CPT2A?/?), an obligate step in mitochondrial long-chain fatty acid CPT2A?/? mice became hypothermic after an acute cold challenge, and CPT2A?/? adipose tissue (BAT) failed to upregulate thermogenic genes in response to stimulation. The adipose-specific loss of CPT2 resulted in diet-dependent in adiposity but did not result in changes in body weight on low- or high-fat Additionally, CPT2A?/? mice had suppressed high-fat diet-induced oxidative and inflammation in visceral white adipose tissue (WAT); however, high-fat glucose intolerance was not improved. These data show that fatty acid oxidation required for cold-induced thermogenesis in BAT and high-fat diet-induced stress and inflammation in WAT.
INSTITUTE
University of Michigan
DEPARTMENT
Biological Chemistry(Johns Hopkins University School of Medicine)
LABORATORY
Wolfgang Lab(Johns Hopkins University School of Medicine)
LAST_NAME
Wolfgang
FIRST_NAME
Michael
ADDRESS
733 North Broadway, Suite G49 Baltimore, MD 21205-2196
EMAIL
mwolfga1@jhmi.edu
PHONE
443-287-7680
NUM_GROUPS
2
TOTAL_SUBJECTS
16
STUDY_COMMENTS
(CPT2A?/?) stands for Carnitine palmitoyltransferase 2 knock out
Short-chain fatty acid analysis in bronchoalveolar lavage fluid (BAL SCFA)
STUDY_TYPE
We will correlate the bacterial gene abundance with the metabolite concentration
STUDY_SUMMARY
The study is intended to find if correlation exists between the abundance of bacterial gene for pyruvate ferredoxin oxidoreductase (PFOR) and short-chain fatty acids concentration in bronchoalveolar lavage fluid from patients with HIV-Associated Bacterial Pneumonia.
INSTITUTE
University of Michigan
DEPARTMENT
Pulmonary Medicine(New York University School of Medicine)
LABORATORY
Weiden Lab(New York University School of Medicine)
LAST_NAME
Weiden
FIRST_NAME
Michael
ADDRESS
New York
EMAIL
michael.weiden@nyumc.org
PHONE
212-263-6479
SUBMIT_DATE
2014-03-26
NUM_GROUPS
2
TOTAL_SUBJECTS
39
STUDY_COMMENTS
PFOR stands for pyruvate ferredoxin oxidoreductase gene
Lung contusion is a major risk factor for the development of acute respiratory syndrome. Hypoxia-inducible factor-1? is the primary transcription factor that responsible for regulating the cellular response to changes in oxygen tension. set to determine if hypoxia-inducible factor-1? plays a role in the of acute inflammatory response and injury in lung contusion.Nonlethal unilateral lung contusion was induced in a hypoxia reporter mouse model and 2 cell-specific hypoxia-inducible factor-1? conditional knockout mice. The mice killed at 5-, 24-, 48-, and 72-hour time points, and the extent of systemic and hypoxia was assessed. In addition, injury and inflammation were assessed by bronchoalveolar lavage cells (flow cytometry and cytospin), albumin injury), and cytokines (inflammation). Isolated type 2 cells from the factor-1? conditional knockout mice were isolated and evaluated for cytokines following lung contusion. Finally, the role of nuclear factor-?B and as intermediates in this interaction was studied.
INSTITUTE
University of Michigan
DEPARTMENT
Surgery
LABORATORY
Raghavendran Lab
LAST_NAME
Thomas
FIRST_NAME
Bivin
ADDRESS
Ann Arbor, MI
EMAIL
bthomas@umich.edu
PHONE
734-615-7142
NUM_GROUPS
4
TOTAL_SUBJECTS
8
STUDY_COMMENTS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245055/ : HIF1 (+/+) stands for reporter mouse modelHIF1 (-/-) stands for type 2 cell-specific factor-1? conditional knockout
Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human IPF & Normal Lung Fiboblasts (Part 2)
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis. Ceramide analysis for parp1 wild type lung tissue/Cells after saline or bleomycin treatment.
STUDY_SUMMARY
This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies (ST000143, ST000183)This specific experiment is a small pilot study to establish method performance, it includes four biological replicas of identical cell cultures after the identical treatment and a single tissue sample.
This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies (ST000199)This specific experiment is a pilot study to compare the metabolism of cells transformed using empty vector against cells transformed with vector carrying short hairpin RNA (shRNA) targeted to silence isocitrate dehydrogenase-1 (IDH1) gene.
The goal of the study was to compare the influence of Ileal pouch-anal (IPAA) surgical treatment on patients with ulcerative colitis (UC) vs those familial adenomatous polyposis (FAP). Stool samples were obtained at the time clinic visit, immediately frozen and stored at -80oC until the assay. There no exclusion criteria.
Small airway epithelial cell (SAEC) (Lonza Walkersville, Inc., MD) were grown according to the manufacturer's instructions in growth medium (SAGM) containing 0.03 mg/ml bovine pituitary extract (BPE), 0.5 µg/ml hydrocortisone, 0.5 ng/ml hEGF, 0.5 µg/ml epinephrine, 10 µg/ml transferrin, 5 µg/ml insulin, 0.1 ng/ml retinoic acid, 6.5ng/ml triiodothyronine, 50 µg/ml gentamicin and 50ng/ml Amphotericin-B, and 0.5 mg/ml bovine serum albumin (BSA, fatty acid free). When SAE grew to around 80 to 90% confluence, the cells were put into basal medium not supplemented with growth factors 3hours. Then the cell monolayers were infected with naïve hMPV at multiplicity of infection (MOI) of 3 to certain time. The supernatant was saved and cells were harvested and stored exactly according to the protocol provided by University of Michigan Metabolomics Core Facility for metabolomics analysis. 50mM ammonium acetate in water was used for rinse buffer.
Small airway epithelial cell (SAEC) (Lonza Walkersville, Inc., MD) were grown according to the manufacturer's instructions in growth medium (SAGM) containing 0.03 mg/ml bovine pituitary extract (BPE), 0.5 µg/ml hydrocortisone, 0.5 ng/ml hEGF, 0.5 µg/ml epinephrine, 10 µg/ml transferrin, 5 µg/ml insulin, 0.1 ng/ml retinoic acid, 6.5ng/ml triiodothyronine, 50 µg/ml gentamicin and 50ng/ml Amphotericin-B, and 0.5 mg/ml bovine serum albumin (BSA, fatty acid free). When SAE grew to around 80 to 90% confluence, the cells were put into basal medium not supplemented with growth factors 3hours. Then the cell monolayers were infected with naïve hMPV at multiplicity of infection (MOI) of 3 to certain time. The supernatant was saved and cells were harvested and stored exactly according to the protocol provided by University of Michigan Metabolomics Core Facility for metabolomics analysis. 50mM ammonium acetate in water was used for rinse buffer.
Pilot Study 13C flux effects when RhoC or RhoA perturbed (13C BCs)
STUDY_TYPE
13C mass isotopomer analysis (flux studies)
STUDY_SUMMARY
Rho-GTPases are small GTP-binding proteins that contribute to the epithelial-to-mesenchymal transition by regulating several cellular processes including organization of the actin cytoskeleton, cell motility, transcription, and cell proliferation. Overexpression of RhoC-GTPases (RhoC) in breast cancer has been implicated in poor disease prognosis due to increased cancer cells invasion, migration, and motility, which warranted its consideration as a therapeutic target for inhibiting breast cancer metastasis. Using silencing RNA (siRNA) molecules to knockdown RhoC expression is a promising approach to inhibit breast cancer metastases.
INSTITUTE
University of Michigan
DEPARTMENT
Internal Medicine
LABORATORY
Merajver Lab
LAST_NAME
Wynn
FIRST_NAME
Michelle
ADDRESS
University Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105
This experiment was performed using the following cohorts: 1) healthy controls, patients with scleroderma at low risk for pulmonary hypertension, 3) pateints scleroderma at high risk for pulmonary hypertension. Whole blood was drawn into stop soilution (1:1 ratio) at rest and again at peak exercise for each subject.
Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling
STUDY_SUMMARY
Colorectal cancer (CRC) is one of the most prevalent and deadly cancers in the Despite an expanding knowledge of its molecular pathogenesis during the past decades, robust biomarkers to enable screening, surveillance, and therapy of CRC are still lacking. In this study, we present a targeted liquid mass spectrometry-based metabolic profiling approach for identifying biomarker that could enable highly sensitive and specific CRC detection using human serum In this targeted approach, 158 metabolites from 25 metabolic pathways of significance were monitored in 234 serum samples from three groups of patients CRC patients, 76 polyp patients, and 92 healthy controls). Partial least analysis (PLS-DA) models were established, which proved to be powerful for CRC patients from both healthy controls and polyp patients. Receiver operating curves generated based on these PLS-DA models showed high sensitivities (0.96 0.89, respectively, for differentiating CRC patients from healthy controls or patients); good specificities (0.80 and 0.88), and excellent areas under the (0.93 and 0.95) were also obtained. Monte Carlo cross validation (MCCV) was applied, demonstrating the robust diagnostic power of this metabolic profiling
In vitro study with AML cell lines that are treated with different concentrations of cytarabine (nucleoside analog). 8 AML cell lines were incubated for 24hr with 0uM, 1uM and 10uM ara-C. After 24hr the cells were washed and pellets were stored in -80°C for genomic and metabolomic analysis.
Maize plants were transformed with endosperm-specific PPDK RNAi knockout constructs to alter starch/protein ratios. Metabolite pool comparisons will be examined from sibling kernels harvested from segregating ears.
Maize plants were grown under three different temperature regimes: 1) normal day / normal night; 2) hot day / normal night; 3) hot day / hot night. Kernels from developing ears were taken 14, 16, 18, 22, 26 and 40 days after pollination.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
Stewart
LAST_NAME
Stewart
FIRST_NAME
Jon D.
ADDRESS
102 Leigh Hall
EMAIL
jds2@chem.ufl.edu
PHONE
352-846-0743
NUM_GROUPS
3
TOTAL_SUBJECTS
47
STUDY_COMMENTS
Normal day / normal night (17 samples); Hot day / normal night (14 samples); Hot day / hot night (17 samples)
LC-MS Based Approaches to Investigate Metabolomic Differences in the Urine of Young Women after Drinking Cranberry Juice or Apple Juice
STUDY_TYPE
drug dosage
STUDY_SUMMARY
Eighteen healthy female college students between 21-29 years old with a normal BMI of 18.5-25 were recruited. Each subject was provided with a list of foods that contained significant amount of procyanidins, such as cranberries, apples, grapes, blueberries, chocolate and plums. They were advised to avoid these foods during the 1-6th day and the rest of the study. On the morning of the 7th day, a first-morning baseline urine sample and blood sample were collected from all human subjects after overnight fasting. Participants were then randomly allocated into two groups (n=9) to consume cranberry juice or apple juice. Six bottles (250 ml/bottle) of juice were given to participants to drink in the morning and evening of the 7th, 8th, and 9th day. On the morning of 10th day, all subjects returned to the clinical unit to provide a first-morning urine sample after overnight fasting. The blood sample was also collected from participants 30 min later after they drank another bottle of juice in the morning. After two-weeks of wash out period, participants switched to the alternative regimen and repeated the protocol. One human subject was dropped off this study because she missed part of her appointments. Another two human subjects were removed from urine metabolomics analyses because they failed to provide required urine samples after juice drinking.The present study aimed to investigate overall metabolic changes caused by procyanidins concentrates from cranberries and apples using a global LCMS based metabolomics approach. All plasma and urine samples were stored at -80oC until analysis.
LC-MS Based Approaches to Investigate Metabolomic Differences in the Plasma of Young Women after Drinking Cranberry Juice or Apple Juice
STUDY_TYPE
drug dosage
STUDY_SUMMARY
Eighteen healthy female college students between 21-29 years old with a normal BMI of 18.5-25 were recruited. Each subject was provided with a list of foods that contained significant amount of procyanidins, such as cranberries, apples, grapes, blueberries, chocolate and plums. They were advised to avoid these foods during the 1-6th day and the rest of the study. On the morning of the 7th day, a first-morning baseline urine sample and blood sample were collected from all human subjects after overnight fasting. Participants were then randomly allocated into two groups (n=9) to consume cranberry juice or apple juice. Six bottles (250 ml/bottle) of juice were given to participants to drink in the morning and evening of the 7th, 8th, and 9th day. On the morning of 10th day, all subjects returned to the clinical unit to provide a first-morning urine sample after overnight fasting. The blood sample was also collected from participants 30 min later after they drank another bottle of juice in the morning. After two-weeks of wash out period, participants switched to the alternative regimen and repeated the protocol. One human subject was dropped off this study because she missed part of her appointments. Another two human subjects were removed from urine metabolomics analyses because they failed to provide required urine samples after juice drinking.The present study aimed to investigate overall metabolic changes caused by procyanidins concentrates from cranberries and apples using a global LCMS based metabolomics approach. All plasma and urine samples were stored at -80oC until analysis.
Vitamin B6 supplementation with 10 mg/d pyridoxine-HCl for 28-d was given to oral contraceptive (OC) users who initially had vitamin B6 deficiency (PLP < 30 nmol/L). Samples are analyzed before and after supplementation. In addition samples from OC users with low (PLP < 30 nmol/L) , middle (PLP 31-99 nmol/L) and high (PLP > 100 nmol/L) vitamin B6 concentration are compared.
Mechanisms of Metabolic Cycles in Diapausing Flesh Fly by Metabolomics Approach
STUDY_TYPE
time course
STUDY_SUMMARY
Insects use diapause, a programmed period of dormancy, to avoid stressful times of the year and to exploit seasonal times of resource availability. Because most diapausing insects do not feed, they must live off their body reserves for several months and the proper use of metabolic reserves is critical for surviving diapause and performing after diapause termination. Across multiple insects, metabolic depression during diapause has been associated with a switch from aerobic metabolism to facultative anaerobic metabolism, despite insects not suffering environmental oxygen limitation. While metabolic rates are depressed during diapause overall to save energy, some insects show regular cyclical bouts of higher metabolic activity during diapause. The functional importance of these metabolic cycles and the mechanisms underlying these cycles are still unknown, but they may be critical for properly maintaining the balance between energy states and purge the accumulation of anaerobic metabolic byproducts. In the present study, we will test the hypothesis that periodic cycles of increased metabolism during insect diapause are associated with both regenerating organismal energetic states, particularly ATP that may decline during metabolic depression, and for purging metabolites associated with anaerobic metabolism. We will use a combination of non-targeted uHPLC-MS/MS metabolomics and targeted NMR-spectroscopy to identify and quantify metabolites that are altered during the cycles in diapausing pupae of the flesh fly, Sarcophaga crassipalpis. This work will allow us to propose specific biochemical and cellular hypotheses for the regulation of cyclic releases from metabolic depression in diapausing insects. Our work may not only reveal the physiological mechanisms regulating metabolic cycles during diapause in flesh fly, but also provide insight to understand the regulation of similar metabolic cycles in mammalian hibernators (i.e., periodic arousal), and also provide insights into how these cycles could be exploited to disrupt the diapause of insect pests.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Chen
FIRST_NAME
Chao
ADDRESS
Department of Entomology and Nematology, Bldg. 970, 1881 Natural Area Dr., Gainesville, FL 32611
Chronic mild stress and Lactobacillus experiments on mice
STUDY_SUMMARY
Mice were devided into three groups (Naive untreated, Stressed untreated, Stressed + Lacto). The stressed groups were subjected to unpredictable chronic mild stress for seven weeks. Three weeks into the protocol, the +Lacto groups were administered probiotic Lactobacillus daily.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Postprandial lipids are lower after vertical sleeve gastrectomy (VSG) surgery and this efect is independent of lipid absorption and chylomicron production. This poses a question of where the lipids are going. In order to test the hypothesis that intestinal oxidation of lipids is increased, Sham or VSG animals were gavaged with glycerol trioleate or water and sacrificed 2h later.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Conjugated linoleic acid (CLA) study in LDLR-/- mice
STUDY_TYPE
Acylcarnitine analysis
STUDY_SUMMARY
LDLR-/- mice were fed a high fat high sucrose diet with either 9,11 CLA or 10,12 CLA. Control groups included no supplementation or caloric restriction to mirror weight loss seen in CLA group. Mice were sacrificed and blood was collected into EDTA tubes. Isolated plasma was immediately frozen at -80C. Adipose tissue from gonadal fat (epididymal white adipose tissue, EWAT) and subcutaneous fat (inguinal white adipose tissue, IWAT) and liver were harvested, snap frozen in liquid nitrogen, and immediately frozen at -80C. An aliquot of thawed plasma was prepared for this project and frozen in an eppendorf tube. Small pieces of frozen tissue were cut and weighed on dry ice and packaged in individual foil packets for this project. **Note: tissue weight is approximate**
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Cecal samples were isolated directly from the ceca of dissected chickens that were either experimentally infected with C. jejuni DRH212 or mock-infected with PBS. Cecal samples were re-suspended in Life Technologies 1X PBS based on weight of sample (1 ml/100 mg = 10-1 dilution) and stored at -80C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
GBM cell lines were plated onto 10 cm dishes at 100,000-200,000 cells per dish and allowed to grow for 3-4 days until confluency reached 50-70%. Media for all cell lines was DMEM with 10% FBS including 25 mM glucose, 6.2 mM glutamine and 200 uM Oleic Acid (conjugated to BSA). 1-2 hours prior to tracer incubation, media was aspirated and fresh media was used. Immediately prior to tracer incubation, media was again aspirated and then cells were washed with warm PBS to remove unlabeled metabolites. Cells were then incubated with labeled tracer (DMEM with 10% FBS including 25 mM Uniformly labeled 13C-6 glucose, 6.2 mM unlabeled glutamine and 200 uM unlabeled oleic acid). After 2 hours of incubation with tracer, media was aspirated, cells were quickly washed with 15 mL DI water, quenched with liquid nitrogen and then stored at -80oC until analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Tumor neurospheres were grown in culture until ~90% confluent. Media was changed to contain 1mM acetate. After 24h, 0h time points were collected and media was changed on all other cells to 1mM 13C-acetate containing media. Cells were then collected at their various time points, 1, 3, 24, 48, or 72 hours. Cells were collected into 15mL tubes, spun down at 100xg for 1min and media aspirated. Pellet was washed (not resuspended) in 150mM ammonium acetate. This was then aspirated off and the cells snap frozen and stored at -80C until all time points complete to ship on dry ice. 0h, 1h, and 3h A, B, and C samples will have gTn by HILIC + TCA by GCMS done on them, while 0h, 1h, and 3h D, E, and F will have FAMES and DG & PC analysis done on them. 24h, 48h, and 72h A, B, and C samples will have FAMES analysis done on them.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human fecal bile acid profiles before and after fecal transplant
STUDY_SUMMARY
Understand the bile acid profiles from the feces of fecal microbiota transplant FMT patients that successfully recover from recurrent C. difficile infection. Submitting fecal samples from patients prior to their FMT and post FMT. Interested in the bile acid profiles of the donor stool that is used in successful transplants. Bile acids are important for C. difficile spore germination and outgrowth.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Early in life exposure studies on human and mouse samples
STUDY_SUMMARY
Experiment1: 2 day old baby mice were exposed to hyperoxia (75% O2) continuously for 7 days. Control baby mice were housed in room air (normoxia). Plasma and bronchoalveolar lavage fluid (BALF) were harvested after 7 days of exposure (on Day of life 9). Experiment2: 2 day old baby mice were exposed to room air or hyperoxia for 14 days and subsequently treated with RV1 or sham.Plasma was collected 5 days after treatment. Human tracheal aspirates were collected from prematurely born infants undergoing mechanical ventilation for respiratory distress syndrome in the first week of life.Tracheal aspirate supernatants are submitted for the assay. We would like to measure adenosine, AMP, ADP and ATP levels.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
13C mass isotopomer analysis (LCMS flux studies) MLL-AF9 (part I)
STUDY_TYPE
1,2-13C2 Flux analysis
STUDY_SUMMARY
How cancer cells adapt to metabolically adverse conditions in patients and strive to proliferate is a fundamental question in cancer biology. Here we show that AMP-activated protein kinase (AMPK), a metabolic checkpoint kinase, confers metabolic stress resistance to leukemia-initiating cells (LICs) and promotes leukemogenesis. Upon dietary restriction, MLL-AF9-induced murine acute myeloid leukemia (AML) activated AMPK and maintained leukemogenic potential. AMPK deletion significantly delayed leukemogenesis and depleted LICs by reducing the expression of glucose transporter 1 (Glut1), compromising glucose flux, and increasing oxidative stress and DNA damage. LICs were particularly dependent on AMPK to suppress oxidative stress in the hypoglycemic bone marrow environment. Strikingly, AMPK inhibition synergized with physiological metabolic stress caused by dietary restriction and profoundly suppressed leukemogenesis. Our results indicate that AMPK protects LICs from metabolic stress and that combining AMPK inhibition with physiological metabolic stress potently suppresses AML by inducing oxidative stress and DNA damage. Research is published: http://www.sciencedirect.com/science/article/pii/S1934590915003744
INSTITUTE
University of Michigan
DEPARTMENT
Molecular and Human genetics (Baylor College of Medicine)
LABORATORY
Nakada Lab (Baylor College of Medicine)
LAST_NAME
Saitoh
FIRST_NAME
Yusuke
ADDRESS
Houston, TX
EMAIL
Yusuke.Saitoh@bcm.edu
PHONE
713-798-1175
NUM_GROUPS
7
TOTAL_SUBJECTS
18
STUDY_COMMENTS
1. Collect leukemia cells from MLL-AF9 leukemia mouse bone marrow. 2. Leukemia cell were cultured in RPMI1640 medium for 16hr. 3. Cell pellets were resuspend in pre-warmed labeling medium containing 1,2-13C2-glucose(2g/L) and incubated for 5min (sample 5) or 60min(sample 60).
Metabolome of three Vancomycin-intermediate Staphylococcus aureus (VISA) mutants compared with the parent strain MM66
STUDY_SUMMARY
Vancomycin-intermediate Staphylococcus aureus (VISA) evolve in a strain-specific manner and acquire mutations that lead to alterations in cell wall metabolism that reduce susceptibility to vancomycin. We had earlier isolated several VISA mutant strains of the clinical hVISA strain MM66. This study is aimed at analyzing the metabolome of these mutants in comparison to the parent strain.
INSTITUTE
Oklahoma State University, Stillwater, OK
LAST_NAME
Gustafson
FIRST_NAME
John
ADDRESS
246C Noble Research Center Oklahoma State University Stillwater, OK 74078-3035
IDH1R132H activity in glioma cell lines and tumnor tissue (2HG)
STUDY_TYPE
Regular
STUDY_SUMMARY
We developed genetically engineered mice to generate brain tumors with especific genetic lessions. The animals were split in three groups: NRAS, P53 knockdown, IDH1-R132H and ATRX knock down (NPAID); NRAS, P53 knockdown, IDH1-R132H (NPI); NRAS, P53 knockdown, (NshP53). From these tumor we obtain and culture tumor cells growth like neurospheres and attached cells.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Muscle Clock knock out mice metabolic changes (iMSBmal1-Exp1)
STUDY_TYPE
Regular
STUDY_SUMMARY
My lab studies the function of the molecular clocks in skeletal muscle. We have an inducible genetic mouse model (C57Bl6 background) in which we knock out the core clock gene, Bmal1, only in adult skeletal muscle after treatment with tamoxifen. We have found that the mice maintain body mass but lose fat mass at 10 weeks after loss of Bmal1. We have done expression profiling on the skeletal muscles and gene expression changes (insulin signaling, CHO metabolism, fat metabolism) suggest significant changes in substrate metabolism. To analyze TCA, CHO metabolites we have collected gastrocnemius muscles from these mice following instructions from Dr. Burant. Mice were anaesthetized with isoflurane, the gastrocnemius muscle dissected and flash frozen with tongs cooled with liquid N2. They have been stored in cryovials in our -80 freezer for 2 months.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Comparison of Metabolites Variation and Antiobesity Effects of a Mixture of Cudrania tricuspidata, Lonicera caerulea, and the Soybean According to Fermentation in vitro and in vivo
STUDY_SUMMARY
We used ultra-performance-liquid-chromatography with quadrupole-time-of-flight mass spectrometry to study the changes in metabolites in the mixture of Cudrania tricuspidata, Lonicera caerulea, and soybean (CLM) during fermentation. Additionally, the antiobesity effects of CLM and fermented-CLM (FCLM) were studied based on the analysis of plasma from high-fat diet (HFD)-fed mice. The levels of cyanidin and the glycosides of luteolin, quercetin, and cyanidin derived from L. caerulea were decreased, whereas the levels of luteolin and quercetin were increased during fermentation. Isoflavone glycosides and soyasaponins originating from the soybean were decreased, whereas their aglycones such as daidzein, glycitein, and genistein were increased. As for prenylated flavonoids from C. tricuspidata, these metabolites were decreased at the early stage of fermentation, and were increased at end of the fermentation. In terms of the functional food product, various metabolites derived from diverse natural products in CLM had complementary effects and demonstrated higher antioxidant and pancreatic lipase inhibition activities by fermentation; these activities were closely related to flavonoid aglycones including genistein, daidzein, glycitein, luteolin, and quercetin. In vivo experiment, several clinical parameters affected by HFD were remarkably improved by the administration of either CLM or FCLM, but there was a difference in the antiobesity effects. The levels of lysoPCs with C20:4, C16:0, and C22:6 were significantly attenuated by CLM administration, while the attenuated levels of lysoPCs with C20:4 and C18:2 were significantly restored by FCLM administration. These metabolites may explain the above-mentioned differences in antiobesity effects. Although only the changes in plasma lysophospholipids could not fully explain antiobesity effects between non-fermented and fermented plant mixtures from our results, we suggest that metabolomics approach could provide a way to reveal the metabolite alterations in the complex fermentation process and understand the differences or changes in bioactivity according to fermentation.
INSTITUTE
Konkuk university
LAST_NAME
Suh
FIRST_NAME
Dong Ho
ADDRESS
Neong-Dong-ro 120, Seoul, Kwang-Gin-gu, 05029, Korea, South
Experiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Allantoin differences in Synechococcus cells grown in high versus low lightgrowth
STUDY_SUMMARY
This experimented consisted of analysis of 500-1000ml of Synechococcus dense cell cultures grown in high versus low light. The goal was to see any differences in the metabolites between the two treatments, especially with respect to Allantoin.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Single treatment gene impact on Arabidopsis metabolites
STUDY_SUMMARY
This experiment aims to measure the impact of the genes that have been introduced into WT lines and compare the metabolic profiling of these plants with WT control plants. Compounds of particular intereset for this study include pyruvate, fumarate, malate, glyoxylate, anthocyanin, carotenes, and lipid compounds.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
This experiment tests the effects of alcoholism by examining the primary metabolites obtained from mouse stool. Stool was collected from 4 groups of mice with varying treatments. One group was not humanized, another was humanized from a healthy human, a third was humanized from a current drinker, and the final group was humanized from a current drinker but also given a treatment of LGG. Humanizations were done to create a model of human gut activity in the mice.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Progesterone level effects on primary metabolites in uterus, blood, and ovaries (Part 1:Plasma)
STUDY_SUMMARY
In this experiment a hormonal protocol was applied to control follicle growth to yield larger or smaller preovulatory follicle and CLs and consequently different circulating Progesterone (P4) concentrations during early diestrus. The two different animal's group are: high or low progesterone levels. The effects of these progesterone levels was tested in the blood of the cow.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Progesterone level effects on primary metabolites in uterus, blood, and ovaries (Part 2:Uterine flush)
STUDY_SUMMARY
In this experiment a hormonal protocol was applied to control follicle growth to yield larger or smaller preovulatory follicle and CLs and consequently different circulating Progesterone (P4) concentrations during early diestrus. The two different animals group are: high or low progesterone levels. The effects of these progesterone levels was tested in the uterus of the cow.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Progesterone level effects on primary metabolites in uterus, blood, and ovaries (Part 3:Ovaries)
STUDY_SUMMARY
In this experiment a hormonal protocol was applied to control follicle growth to yield larger or smaller preovulatory follicle and CLs and consequently different circulating Progesterone (P4) concentrations during early diestrus. The two different animal's group are: high or low progesterone levels. The effects of these progesterone levels was tested in the ovaries (follicle fluid) of the cow.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic effects of metformin on mouse liver, intestine, and serum
STUDY_SUMMARY
Experiment to test the different metabolomic effects of two different doses of metformin (50mg vs 150 mg). A saline treatment group was used as a control. The effects were measured at the liver, intestine, and serum of the mouse.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Role of medium in bacterial growth (HILIC chromatography)
STUDY_SUMMARY
Experiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Primary metabolites at different points along dog gastrointestinal tract
STUDY_SUMMARY
This experiment tests the primary metabolites at four different points along the gastrointestinal tract of a dog. The four points being tested were the duodenum, ileum, colon, and rectum.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Primary metabolites at different points along dog gastrointestinal tract (RP chromatography)
STUDY_SUMMARY
This experiment tests the primary metabolites at four different points along the gastrointestinal tract of a dog. The four points being tested were the duodenum, ileum, colon, and rectum.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
This experiment tested the affects of different diets on mice esophagus metabolites. The diets ranged from zinc sufficient to zinc deficient and a third group that included zinc deficient mice that were put back on zinc sufficient diets.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Effects of Zinc on GI tract metabolites (Part 2: Prostate)
STUDY_SUMMARY
This experiment tested the affects of different diets on mice prostate metabolites. The diets ranged from zinc sufficient to zinc deficient and a third group that included zinc deficient mice that were put back on zinc sufficient diets.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
This experiment aimed to see the effects of Giardia Intestinalis on the small intestine of mice. The metabolites of the proximal and distal ends of the small intestine of healthy mice were compared to those of mice who had been infected with Giardia intestinalis for 7 days.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomics of bovine uterine fluid at the onset of conceptus elongation
STUDY_TYPE
Prospective cohort study
STUDY_SUMMARY
The objective is to investigate changes in metabolomics of uterine lumen content of lactating dairy cows associated with the onset of conceptus (embryo and associated membranes) elongation. Lactating dairy cows had estrous cycles synchronized and were subjected to induced ovulation and timed artificial insemination (AI). The day of AI was considered study d 0. On d 15, uteri were flushed by transcervical catheterization and infusion of 20 mL of phosphate buffered solution with 0.1% of polyvinyl acetate. Recovered conceptuses were classified based on morphology/length as ovoid (OV; 1-4 mm), tubular (TUB; 5-19 mm) and filamentous (FIL; 20-85 mm). The first 20 mL infused in the uterus were recovered, placed in conical tubes and centrifuged at 2,000 × g at 4ᵒC. The supernatant was collect, aliquoted and stored at -80ᵒC for later analyses of fluid composition, including measurement of IFN-τ concentration. Cows with no conceptus recovered and no detection of IFN-τ in uterine flushing were considered as nonpregnant (NPREG). The experimental design was then considered a prospective cohort study with 4 independent groups (NPREG, OV, TUB, and FIL). The additional 5th group represents a specific physiological condition of cows within the study and it will be compared to TUB and FIL groups combined, working as a pilot study for future research.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
Laboratory of Reproduction and Nutrition of Dairy Cows
Metabolomics Approach to Allograft Assessment in Liver Transplantation
STUDY_TYPE
Retrospective analysis of biobanked liver tissue from organ donors
STUDY_SUMMARY
This pilot study is designed to apply several types of metabolomic analysis for liver allograft assessment with the aim of identifying candidate biomarkers for allograft function and to develop a methodology that could be applied to larger scale studies. The three main categories of metabolomic analysis are reflected in each of the specific aims, including a targeted profiling of central carbon metabolism, open lipidomic and metabolomic profiling for hypothesis generation and MALDI-IMS for tissue-based spatial analysis. Each of these approaches offers potential benefits that could be optimized in a protocol for larger scale studies depending the results of the pilot investigations.
INSTITUTE
Ochsner Multi-Organ Transplant Institute
DEPARTMENT
SECIM
LABORATORY
Abdominal Organ Transplantation
LAST_NAME
Seal
FIRST_NAME
John
ADDRESS
1514 Jefferson Highway, New Orleans, LA 70121
EMAIL
John.Seal@ochsner.org
PHONE
504-232-4253
NUM_GROUPS
3
TOTAL_SUBJECTS
Targeted analysis and open profiling: Control group - standard criteria donor (N=15); Experimental group - donation-after-cardiac-death donors (N=10). MALDI-IMS - standard criteria donor (N=10)
Unbiased profiling uncovers a crucial role for gut microbiome derived metabolites in modulating GI epithelial cell damage and mitigating GVHD.
STUDY_SUMMARY
Taxonomic alterations in the intestinal microbiota are being progressively associated with many diseases, including graft-versus host disease (GVHD). However, the impact of these alterations on microbial metabolites and by-products and their subsequent impact on disease processes, such as GVHD, are not known. Here we utilized a targetedn unbiased and blinded approach in a blinded fashion to identify novel alterations in the levels of microbial metabolites, specifically levels including the short chain fatty acid (SCFA) and endogenous histone deacetylase inhibitor (HDACi), butyrate, after allo-BMT. Surprisingly, alterations were observed only in intestinal epithelial cells (IECs) but not in the luminal contents. The reduced butyrate in IECs (CD326+) after allo-BMT resulted in decreased histone acetylation, which was restored upon local administration of exogenous butyrate. This resulted in improved IEC junctional integrity, increased anti-apoptotic proteins, decreased GVHD, and improved survival. Furthermore, alteration of endogenous microflora with 17 rationally selected strains of high butyrate producing Clostridia, also decreased GVHD and increased survival following allo-BMT in experiments performed at two different institutions. These data demonstrate an heretofore unrecognized role of microbial metabolites and suggests that local and specific alteration of microbial metabolites has direct salutary effects on GVHD target tissues and mitigates its severity.
This experiment aimed to discover the effects of metformin on mouse liver and kidney tissue. The effects were seen by comparing the liver of the metformin group to the liver of a control group of mice treated given saline solution.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Renal metabolic pathways indicating ischemic or inflammatory changes
STUDY_SUMMARY
Tissues were acquired from kidkeys that were deemed unsuitable for transplant and were then analyzed by the lab through normothermic machine perfusion. They were perfused with either whole blood perfusate or with packed red blood cell perfusate. These tissues' metabolic pathways were then analyzed for markers of ischemic or inflammatory responses in the renal tissue
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Modification of metabolites by gut microbiota in response to diet
STUDY_SUMMARY
This experiment is looking at effects of diets on rats. Specifically how those diets might alter metabolites that could be modified by gut microbiota and in particular indoles and bile salts.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Effects of dietary supplement on hamster metabolism
STUDY_SUMMARY
This experiment aims to analyze spent media from a protein over-expression system. The treatment was a lipid supplement given to hamsters. The spent media was then analyzed to see how the lipid supplement affected lipid metabolism.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolites detected from human bronchoalveolar lavage
STUDY_SUMMARY
This is a preliminary trial to determine how viable this system will be to use on a much larger number of samples (up to 150). We would like to determine the range, number of metabolite species, and relative concentrations than can be detected in human bronchoalveolar lavage. We would also like to determine how clear the distinction is between the 3 patient groups as this will inform us as to how many of the 150 samples we need to run in the study proper.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic analysis on samples from rats expressing human amylin (cardiac tissue).
STUDY_SUMMARY
Human amylin proteotoxicity impairs protein biosynthesis, and alters major cellular signaling pathways in the heart, brain and liver of humanized diabetic rat model in vivo. The 37 amino acid hormone Amylin is cosecreted with insulin from ß cells in the pancreas. In prediabetic and obese humans, chronic amylin hypersecretion parallels the course of disease and is involved in the pathophysiology of beta cell destruction in the pancreas. Recent studies in rats with transgenic expression of beta cell amylin (HIP), we have discovered that human amylin is prone to misfolding and has proteotoxic effects in vivo, resulting in the induction of cell death paralleling the pathophysiology of neurodegenerative disease. These misfolded proteotoxic amylin proteins are found to migrate to both the brain and heart to induce both neurologic deficits and cardiac dysfunction. In the present study, we use nontargeted GCMS metabolomics analysis to investigate the metabolic consequences of amyloidogenic and cytotoxic amylin oligomers and diabetes in HIP heart, brain, liver, and plasma compared to wild type controls at 1 year of age. We identified that HIP hearts had 45 significantly altered metabolites by ttest (p<0.05) compared to wildtype control hearts (0.134.3 fold different,N=8/group). Similarly, we identified 30 metabolites significantly different in the HIP brain by ttest (p<0.05) compared to wildtype control brains (0.225.2 fold different (N=~10/group). HIP livers had 58 metabolites significantly altered by ttest (p<0.05) compared to wildtype livers (0.0199.4 fold different,N=~10/group. Pathway enrichment analysis identified a systemic alteration in protein biosynthesis in the heart and brain of HIP rats compared to wild type controls. Alterations in phenylalanine metabolism and aminoacyltRNA biosynthesis were specifically affected in heart and plasma. Tyrosine metabolism is affected across organs, including decreased tyrosine (heart), phenylalanine (heart, liver, brain), and increased fumarate (heart, liver, brain). Increased urea and urea cycle were identified in heart and liver. As protein degradation is a major upregulator of the urea cycle in human rat diabetic models, these findings suggest a broader connection between amylin, diabetes, protein catabolism, and effects on the urea cycle, which may contribute to the increased morbidity and mortality in diabetics at a multisystem level beyond the effects on glucose metabolism.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Ilaiwy
FIRST_NAME
Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Metabolomic analysis on samples from rats expressing human amylin (brain tissue).
STUDY_TYPE
Non targeted metabolomics-Brain tissue
STUDY_SUMMARY
Human amylin proteotoxicity impairs protein biosynthesis, and alters major cellular signaling pathways in the heart, brain and liver of humanized diabetic rat model in vivo. The 37 amino acid hormone Amylin is cosecreted with insulin from ß cells in the pancreas. In prediabetic and obese humans, chronic amylin hypersecretion parallels the course of disease and is involved in the pathophysiology of beta cell destruction in the pancreas. Recent studies in rats with transgenic expression of beta cell amylin (HIP), we have discovered that human amylin is prone to misfolding and has proteotoxic effects in vivo, resulting in the induction of cell death paralleling the pathophysiology of neurodegenerative disease. These misfolded proteotoxic amylin proteins are found to migrate to both the brain and heart to induce both neurologic deficits and cardiac dysfunction. In the present study, we use nontargeted GCMS metabolomics analysis to investigate the metabolic consequences of amyloidogenic and cytotoxic amylin oligomers and diabetes in HIP heart, brain, liver, and plasma compared to wild type controls at 1 year of age. We identified that HIP hearts had 45 significantly altered metabolites by ttest (p<0.05) compared to wildtype control hearts (0.134.3 fold different,N=8/group). Similarly, we identified 30 metabolites significantly different in the HIP brain by ttest (p<0.05) compared to wildtype control brains (0.225.2 fold different (N=~10/group). HIP livers had 58 metabolites significantly altered by ttest (p<0.05) compared to wildtype livers (0.0199.4 fold different,N=~10/group. Pathway enrichment analysis identified a systemic alteration in protein biosynthesis in the heart and brain of HIP rats compared to wild type controls. Alterations in phenylalanine metabolism and aminoacyltRNA biosynthesis were specifically affected in heart and plasma. Tyrosine metabolism is affected across organs, including decreased tyrosine (heart), phenylalanine (heart, liver, brain), and increased fumarate (heart, liver, brain). Increased urea and urea cycle were identified in heart and liver. As protein degradation is a major upregulator of the urea cycle in human rat diabetic models, these findings suggest a broader connection between amylin, diabetes, protein catabolism, and effects on the urea cycle, which may contribute to the increased morbidity and mortality in diabetics at a multisystem level beyond the effects on glucose metabolism.
INSTITUTE
Duke University
DEPARTMENT
Sarah W. Stedman Nutrition and Metabolism Center
LABORATORY
Metabolomics lab
LAST_NAME
Ilaiwy
FIRST_NAME
Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
amroilaiwy@gmail.com, monte_willis@med.unc.edu
PHONE
210-596-0171
STUDY_COMMENTS
Brain tissue-Metabolomic analysis was performed at Duke Metabolomics lab
Metabolomic analysis on samples from rats expressing human amylin (hepatic tissue).
STUDY_SUMMARY
Human amylin proteotoxicity impairs protein biosynthesis, and alters major cellular signaling pathways in the heart, brain and liver of humanized diabetic rat model in vivo. The 37 amino acid hormone Amylin is cosecreted with insulin from ß cells in the pancreas. In prediabetic and obese humans, chronic amylin hypersecretion parallels the course of disease and is involved in the pathophysiology of beta cell destruction in the pancreas. Recent studies in rats with transgenic expression of beta cell amylin (HIP), we have discovered that human amylin is prone to misfolding and has proteotoxic effects in vivo, resulting in the induction of cell death paralleling the pathophysiology of neurodegenerative disease. These misfolded proteotoxic amylin proteins are found to migrate to both the brain and heart to induce both neurologic deficits and cardiac dysfunction. In the present study, we use nontargeted GCMS metabolomics analysis to investigate the metabolic consequences of amyloidogenic and cytotoxic amylin oligomers and diabetes in HIP heart, brain, liver, and plasma compared to wild type controls at 1 year of age. We identified that HIP hearts had 45 significantly altered metabolites by ttest (p<0.05) compared to wildtype control hearts (0.134.3 fold different,N=8/group). Similarly, we identified 30 metabolites significantly different in the HIP brain by ttest (p<0.05) compared to wildtype control brains (0.225.2 fold different (N=~10/group). HIP livers had 58 metabolites significantly altered by ttest (p<0.05) compared to wildtype livers (0.0199.4 fold different,N=~10/group. Pathway enrichment analysis identified a systemic alteration in protein biosynthesis in the heart and brain of HIP rats compared to wild type controls. Alterations in phenylalanine metabolism and aminoacyltRNA biosynthesis were specifically affected in heart and plasma. Tyrosine metabolism is affected across organs, including decreased tyrosine (heart), phenylalanine (heart, liver, brain), and increased fumarate (heart, liver, brain). Increased urea and urea cycle were identified in heart and liver. As protein degradation is a major upregulator of the urea cycle in human rat diabetic models, these findings suggest a broader connection between amylin, diabetes, protein catabolism, and effects on the urea cycle, which may contribute to the increased morbidity and mortality in diabetics at a multisystem level beyond the effects on glucose metabolism.
INSTITUTE
University of North Carolina
LABORATORY
Multiple Centers
LAST_NAME
Ilaiwy
FIRST_NAME
Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Metabolomic analysis on samples from rats expressing human amylin (plasma).
STUDY_SUMMARY
Human amylin proteotoxicity impairs protein biosynthesis, and alters major cellular signaling pathways in the heart, brain and liver of humanized diabetic rat model in vivo. The 37 amino acid hormone Amylin is cosecreted with insulin from ß cells in the pancreas. In prediabetic and obese humans, chronic amylin hypersecretion parallels the course of disease and is involved in the pathophysiology of beta cell destruction in the pancreas. Recent studies in rats with transgenic expression of beta cell amylin (HIP), we have discovered that human amylin is prone to misfolding and has proteotoxic effects in vivo, resulting in the induction of cell death paralleling the pathophysiology of neurodegenerative disease. These misfolded proteotoxic amylin proteins are found to migrate to both the brain and heart to induce both neurologic deficits and cardiac dysfunction. In the present study, we use nontargeted GCMS metabolomics analysis to investigate the metabolic consequences of amyloidogenic and cytotoxic amylin oligomers and diabetes in HIP heart, brain, liver, and plasma compared to wild type controls at 1 year of age. We identified that HIP hearts had 45 significantly altered metabolites by ttest (p<0.05) compared to wildtype control hearts (0.134.3 fold different,N=8/group). Similarly, we identified 30 metabolites significantly different in the HIP brain by ttest (p<0.05) compared to wildtype control brains (0.225.2 fold different (N=~10/group). HIP livers had 58 metabolites significantly altered by ttest (p<0.05) compared to wildtype livers (0.0199.4 fold different,N=~10/group. Pathway enrichment analysis identified a systemic alteration in protein biosynthesis in the heart and brain of HIP rats compared to wild type controls. Alterations in phenylalanine metabolism and aminoacyltRNA biosynthesis were specifically affected in heart and plasma. Tyrosine metabolism is affected across organs, including decreased tyrosine (heart), phenylalanine (heart, liver, brain), and increased fumarate (heart, liver, brain). Increased urea and urea cycle were identified in heart and liver. As protein degradation is a major upregulator of the urea cycle in human rat diabetic models, these findings suggest a broader connection between amylin, diabetes, protein catabolism, and effects on the urea cycle, which may contribute to the increased morbidity and mortality in diabetics at a multisystem level beyond the effects on glucose metabolism.
INSTITUTE
University of North Carolina
LABORATORY
Multiple Centers
LAST_NAME
Ilaiwy
FIRST_NAME
Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Determining the metabolic profile of wildtype, lrgAB, and atlA mutant Steptococcus mutans grown aerobically and anaerobically
STUDY_TYPE
Single time point, aerobic vs. anaerobic cultures
STUDY_SUMMARY
Whole cells from both aerobic and anaerobic cultures of wild-type,lrgAB and atlA strain will be isolated for analysis of the whole cytosolic metabolome. Supernatants will be also analyzed for their metabolite profile in wild type and lrgAB cultures.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Ahn
FIRST_NAME
Sang-Joon
ADDRESS
1395 Center Drive, Room D5-29 Gainesville FL 32610
The Development of Metabolomic Markers in African Bermudagrass (C. transvaalensis) for Sting Nematode (Belonolaimus longicaudatus) Response
STUDY_TYPE
Disease response in terms of nematode reproduction and root weight
STUDY_SUMMARY
The objective of the proposed pilot study is to identify metabolites up- and down-regulated in African bermudagrass that are tolerant and sensitive to the sting nematode and develop metabolomic markers for the highest expressed metabolites associated with tolerance. Future work will include additional accessions and species of bermudagrass, and testing under field conditions. Bermudagrass accessions identified as tolerant or sensitive by Pang et al. (2011) will be assessed under controlled greenhouse conditions to identify metabolites linked to sting nematode tolerance. Nematode response will be quantified through determination of root length and weight and the number of nematodes present 136 days after inoculation. Higher root length and weight indicate tolerance or resistance. Higher nematode counts indicate greater reproduction (i.e. a susceptible plant), while lower counts indicate that the accession may have some resistance. Metabolites from root tissue of these accessions will be compared to identify those associated with tolerance/resistance, and those that are associated with nematode infestation by comparing inoculated plants to uninoculated controls. Metabolomic markers will then be developed for the metabolites associated with tolerance/resistance. These markers will be used to guide future screening of bermudagrass accessions for breeding nematode-tolerant or -resistant varieties.
Metabolite comparison of mouse gastric tissue and glands
STUDY_SUMMARY
The goal of this project was to compare the metabolite profiles of the: mouse gastric antrum and the mouse gastric corpus, the mouse gastric antrum and the mouse gastric antrum isolated glands, and the mouse gastric corpus and the mouse gastric corpus isolated glands.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Broad Spectrum MS analysis of mouse hypothalmus from Anxiety Prone HSV-Latently Infected Obese Mice
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Brain tissue samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and brain tissue samples were collected and processed for metabolomics.
Broad Spectrum MS analysis of mouse hippocampus from Anxiety Prone HSV-Latently Infected Obese Mice
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Brain tissue samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and brain tissue samples were collected and processed for metabolomics.
Broad Spectrum MS analysis of mouse microglia cells from Anxiety Prone HSV-Latently Infected Obese Mice
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
A mouse model of obese HSV-1 latent infection was developed. Broad spectrum metabolomics analysis was performed to better understand the metabolomic profile of microglia cells and to compare this metabolomics profile with that of the hippocampus, hypothalamus, and peripheral blood mononuclear cells. Microglia cell samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and microglia cell samples were collected and processed for metabolomics.
Characterization and Plasticity of the Metabolome in Peripheral Cells in Bipolar I Disorder
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Patients with Bipolar I Disorder (BPI) and matched non-affected controls were recruited. Males and females from all races and ethnicities between the ages of 19-65 participated in the research. Skin biopsies were obtained and fibroblasts were isolated from each of these biopsies. A total of 1 x 〖10〗^7 fibroblasts cells were used for metabolomics. Cell pellets were flash frozen in liquid nitrogen and shipped on dry ice to the NIH Eastern Regional Comprehensive Metabolomic Resource Core at RTI International in North Carolina. Metabolomics will be determined using a broad spectrum metabolomics protocol by RTI
Associations between 69 Sphingolipids and Emphysema, Chronic Bronchitis, Exacerbations, and FEV1/FVC
STUDY_TYPE
Association Study
STUDY_SUMMARY
One hundred twenty-nine current and former smokers from the COPDGene cohort had 69 distinct sphingolipid species detected in plasma by targeted mass spectrometry. Of these, 23 were also measured in 131 plasma samples (117 independent subjects) using an untargeted platform in an independent laboratory. Regression analysis with adjustment for clinical covariates, correction for false discovery rate, and metaanalysis were used to test associations between COPD subphenotypes and sphingolipids. Peripheral blood mononuclear cells were used to test associations between sphingolipid gene expression and plasma sphingolipids.
Broad Spectrum MS analysis of mouse peripheral blood mononuclear cells (PBMC) from Anxiety Prone HSV-Latently Infected Obese Mice
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Mononuclear cell samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and mononuclear cell samples were collected and processed for metabolomics.
Distinctly perturbed metabolic networks underlie differential tumor tissue damages induced by immune modulator b-glucan in a two-case ex vivo non-small cell lung cancer study
STUDY_TYPE
tracer
STUDY_SUMMARY
[U-13C]-Glu SIRM study of ex vivo tissue slices in matched-pair tumor/non-tumor ex vivo tissue slices from two human patients with and withou beta-glucan.
INSTITUTE
University of Kentucky
DEPARTMENT
CESB
LAST_NAME
Fan
FIRST_NAME
Teresa
ADDRESS
Rm 516 Biopharm Complex, 789 S. Limestone St.,Univ. of Kentucky, Lexington, KY 40536
Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer
STUDY_TYPE
Lung cancer case control biomarker discovery
STUDY_SUMMARY
Recently, the National Lung Cancer Screen Trial (NLST) demonstrated that low-dose CT (LDCT) screening could reduce mortality due to lung cancer by 20%. However, LDCT screening is largely hindered by high false-positive rates (96%), particularly in high-risk populations (heavy smokers), due to the low prevalence rates (less than 2%) of malignant tumors and high incidence of benign lung nodules. Consequently, complementary biomarkers that can be used in conjunction with LDCT screening to improve diagnostic capacities and reduce false-positive rates are highly desirable. Preferably, such complementary tools should be noninvasive and exhibit high sensitivity and specificity. The application of “-omic” sciences (genomics, transcriptomics, proteomics, and metabolomics) represents valuable tools for the discovery and validation of potential biomarkers that can be used for detection of NSCLC. Of these omic sciences, metabolomics has received considerable attention for its application in cancer. Metabolomics is the assessment of small molecules and biochemical intermediates (metabolites) using analytic instrumentation. Metabolites in blood are the product of all cellular processes, which are highly responsive to conditions of disease and environment, and represent the final output products of all organs forming a detailed systemic representation of an individual's current physiologic state. In this study, we used an untargeted metabolomics approach using gas chromatography time-of-flight mass spectrometry (GCTOFMS) to analyze the metabolome of serum and plasma samples both collected from the same patients that were organized into two independent case–control studies (ADC1 and ADC2). In both studies, only NSCLC adenocarcinoma was investigated. The overall objectives were to (i) determine whether individual or combinations of metabolites could be used as a diagnostic test to distinguish NSCLC adenocarcinoma from controls and (ii) to determine which, plasma or serum, provides more accurate classifiers for the detection of lung cancer. We developed individual and multimetabolite classifiers using a training test from the ADC1 study and evaluated the performance of the constructed classifiers, individually or in combination, in an independent test/validation study (ADC2). This study shows the potential of metabolite-based diagnostic tests for detection of lung adenocarcinoma. Further validation in a larger pool of samples is warranted.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control The first set (ADC1) used for biomarker development consisted of serum and plasma samples obtained from 52 stages I–IV NSCLC adenocarcinoma patients (52 plasma and 49 serum), and 31 healthy controls (31 pairs of serum and plasma) for a total of 163 samples. This set was regarded as the training set for biomarker discovery and classifier development. A second, independent case–control study (ADC2) consisting of serum and plasma samples collected from 43 stage I–IV NSCLC adenocarcinoma patients and 43 healthy controls (total 172 samples) was used as an independent test set for biomarker evaluation. A limitation of this study is the relatively small sample size for each cohort (52 cases, 31 controls for ADC1, and 43 cases and 43 controls for ADC2) because patient variability can be a big factor in smaller studies.
Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer (part II)
STUDY_TYPE
Lung cancer case control biomarker discovery
STUDY_SUMMARY
Recently, the National Lung Cancer Screen Trial (NLST) demonstrated that low-dose CT (LDCT) screening could reduce mortality due to lung cancer by 20%. However, LDCT screening is largely hindered by high false-positive rates (96%), particularly in high-risk populations (heavy smokers), due to the low prevalence rates (less than 2%) of malignant tumors and high incidence of benign lung nodules. Consequently, complementary biomarkers that can be used in conjunction with LDCT screening to improve diagnostic capacities and reduce false-positive rates are highly desirable. Preferably, such complementary tools should be noninvasive and exhibit high sensitivity and specificity. The application of “-omic” sciences (genomics, transcriptomics, proteomics, and metabolomics) represents valuable tools for the discovery and validation of potential biomarkers that can be used for detection of NSCLC. Of these omic sciences, metabolomics has received considerable attention for its application in cancer. Metabolomics is the assessment of small molecules and biochemical intermediates (metabolites) using analytic instrumentation. Metabolites in blood are the product of all cellular processes, which are highly responsive to conditions of disease and environment, and represent the final output products of all organs forming a detailed systemic representation of an individual's current physiologic state. In this study, we used an untargeted metabolomics approach using gas chromatography time-of-flight mass spectrometry (GCTOFMS) to analyze the metabolome of serum and plasma samples both collected from the same patients that were organized into two independent case–control studies (ADC1 and ADC2). In both studies, only NSCLC adenocarcinoma was investigated. The overall objectives were to (i) determine whether individual or combinations of metabolites could be used as a diagnostic test to distinguish NSCLC adenocarcinoma from controls and (ii) to determine which, plasma or serum, provides more accurate classifiers for the detection of lung cancer. We developed individual and multimetabolite classifiers using a training test from the ADC1 study and evaluated the performance of the constructed classifiers, individually or in combination, in an independent test/validation study (ADC2). This study shows the potential of metabolite-based diagnostic tests for detection of lung adenocarcinoma. Further validation in a larger pool of samples is warranted.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control The first set (ADC1) used for biomarker development consisted of serum and plasma samples obtained from 52 stages I–IV NSCLC adenocarcinoma patients (52 plasma and 49 serum), and 31 healthy controls (31 pairs of serum and plasma) for a total of 163 samples. This set was regarded as the training set for biomarker discovery and classifier development. A second, independent case–control study (ADC2) consisting of serum and plasma samples collected from 43 stage I–IV NSCLC adenocarcinoma patients and 43 healthy controls (total 172 samples) was used as an independent test set for biomarker evaluation. A limitation of this study is the relatively small sample size for each cohort (52 cases, 31 controls for ADC1, and 43 cases and 43 controls for ADC2) because patient variability can be a big factor in smaller studies.
Labeling of cells was carried out in triplicate with each sample containing 35e6. Cells were deprived of glucose or glutamine for 1 h then resuspended in 10mM [13C1,2] D-glucose labeled or 4 mM [13C5]-U-glutamine labeled medium, respectively. At this time cells were also activated with 5 ug/ml anti-CD3 and anti-CD28. Cells were labeled (and activated) for 16 h when samples were spun down, and cells were resuspended in 200 ul ice cold methanol. For this part of the experiment, the spent medium was collected for analysis. All samples were immediately stored in -80oC.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research
LABORATORY
Core Facilities Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
There are 4 germfree controls and 4 germfree with bacteria. After treatment, the mouse stool samples were collected at different timepoints: day 0, day 10, day 26, day 47, and day 61 or 70. Place the stool samples into liquid nitrogen after they were collected, then stored in -80oC.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Measure change in metabolites based on diet and feeding status
STUDY_TYPE
Regular
STUDY_SUMMARY
Flies were fed a normal diet or high-sugar (30% sucrose) diet for 10 days. Flies of each diet were flash frozen in liquid nitrogen as sated (refed for 3hrs on 400mM D-glucose) or after fasting for 24hrs. Heads and bodies were separated using a sieve-system and placed immediately on dry ice (total time app. 1min). We collected 50 heads per condition (4 conditions total) and 5 biological replicates
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Measure change in metabolites based on diet and feeding status (part II)
STUDY_TYPE
Regular
STUDY_SUMMARY
Flies were fed a normal diet or high-sugar (30% sucrose) diet for 10 days. Flies of each diet were flash frozen in liquid nitrogen as sated (refed for 3hrs on 400mM D-glucose) or after fasting for 24hrs. Heads and bodies were separated using a sieve-system and placed immediately on dry ice (total time app. 1min). We collected 50 heads per condition (4 conditions total) and 5 biological replicates
Mice were run for 15 minutes on a treadmill and then mice were induced into anesthesia at a dose of 5% isoflurane, then maintained by continuous inhalation of 2% isoflurane. Quadriceps muscle was collected first and flash frozen in liquid nitrogen. Then blood was collected from the left ventricle of the heart and placed into serum separating tubes. Blood was allowed to clot for 40 minutes and centrifuged, the supernatant was frozen in liquid nitrogen
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Facilities Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Mice were run for 15 minutes on a treadmill and then mice were induced into anesthesia at a dose of 5% isoflurane, then maintained by continuous inhalation of 2% isoflurane. Quadriceps muscle was collected first and flash frozen in liquid nitrogen. Then blood was collected from the left ventricle of the heart and placed into serum separating tubes. Blood was allowed to clot for 40 minutes and centrifuged, the supernatant was frozen in liquid nitrogen
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We use ChAT(BAC)-EGFP mice, which express enhanced green fluorescent protein (EGFP) under the control of transcriptional regulatory elements for choline acetyltransferase (ChAT), the sole enzyme that catalyzes the biosynthesis of acetylcholine (ACh). These mice were treated with inducers of ChAT. Kidney were rapidly removed, frozen on liquid nitrogen and stored at -80C
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Rats were treated with donepezil (DPZ) after the induction of a model of glomerulonephritis (GN) to increase kidney ACh levels. Rats were euthanized at day 25 after the induction of the disease. Kidneys were rapidly removed, frozen in liquid nitrogen and stored at -80C
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
2 hydroxiglutarate with with IDH1-R132H inhibitor in neurospheres
STUDY_TYPE
Regular
STUDY_SUMMARY
Tumor neurospheres carrying genetic lession NPI (NRAS, shP53, IDH1-R132H) colony 1 and 2 (C1 and C2); NPAI (NRAS, shP53, shATRX, IDH1-R132H) colony 1 and 2 (C1 and C2); and NPA (NRAS, shP53, shATRX) (C1 and C2). Was treated with IDH1-R132H inhibitor. By 2HG assay we want to check the effect of the inhibitor in our cells.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
3
TOTAL_SUBJECTS
12
STUDY_COMMENTS
(shATRX) : ATRX knockdown sequence into a Sleeping Beauty (SB) transposase-responsive plasmid
Temporal metabolomic responses of cultured HepG2 liver cells to high fructose and high glucose exposures
STUDY_SUMMARY
High fructose consumption has been implicated with deleterious effects on human health, including hyperlipidemia elicited through de novo lipogenesis. However, more global effects of fructose on cellular metabolism have not been elucidated. In order to explore the metabolic impact of fructose-containing nutrients, we applied both GC-TOF and HILIC-QTOF mass spectrometry metabolomic strategies using extracts from cultured HepG2 cells exposed to fructose, glucose, or fructose + glucose. Cellular responses were analyzed in a time-dependent manner, incubated in media containing 5.5 mM glucose + 5.0 mM fructose in comparison to controls incubated in media containing either 5.5 mM glucose or 10.5 mM glucose. Mass spectrometry identified 156 unique known metabolites and a large number of unknown compounds, which revealed metabolite changes due to both utilization of fructose and high-carbohydrate loads independent of hexose structure. Fructose was shown to be partially converted to sorbitol, and generated higher levels of fructose-1-phosphate as a precursor for glycolytic intermediates. Differentially regulated ratios of 3-phosphoglycerate to serine pathway intermediates in high fructose media indicated a diversion of carbon backbones away from energy metabolism. Additionally, high fructoseconditions changed levels of complex lipids toward phosphatidylethanolamines. Patterns of acylcarnitines in response to high hexose exposure (10.5 mM glucose or glucose/fructose combination) suggested a reduction in mitochondrial beta-oxidation.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Temporal metabolomic responses of cultured HepG2 liver cells to high fructose and high glucose exposures
STUDY_SUMMARY
High fructose consumption has been implicated with deleterious effects on human health, including hyperlipidemia elicited through de novo lipogenesis. However, more global effects of fructose on cellular metabolism have not been elucidated. In order to explore the metabolic impact of fructose-containing nutrients, we applied both GC-TOF and HILIC-QTOF mass spectrometry metabolomic strategies using extracts from cultured HepG2 cells exposed to fructose, glucose, or fructose + glucose. Cellular responses were analyzed in a time-dependent manner, incubated in media containing 5.5 mM glucose + 5.0 mM fructose in comparison to controls incubated in media containing either 5.5 mM glucose or 10.5 mM glucose. Mass spectrometry identified 156 unique known metabolites and a large number of unknown compounds, which revealed metabolite changes due to both utilization of fructose and high-carbohydrate loads independent of hexose structure. Fructose was shown to be partially converted to sorbitol, and generated higher levels of fructose-1-phosphate as a precursor for glycolytic intermediates. Differentially regulated ratios of 3-phosphoglycerate to serine pathway intermediates in high fructose media indicated a diversion of carbon backbones away from energy metabolism. Additionally, high fructoseconditions changed levels of complex lipids toward phosphatidylethanolamines. Patterns of acylcarnitines in response to high hexose exposure (10.5 mM glucose or glucose/fructose combination) suggested a reduction in mitochondrial beta-oxidation.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
This West Coast Metabolomics Center sponsored pilot grant goal is to identify and validate interstitial cystitis/painful bladder syndrome (IC/PBS)-associated urinary metabolites. Our central hypothesis is that IC/PBS-associated metabolites in the urine of IC/PBS patients can segregate patients from control subjects, and that their levels are correlated with clinical symptoms. To test this hypothesis, we will identify IC/PBS-associated metabolites in urine using two independent platforms, GC-MS and quadrupole time-of-flight (Q-TOF) mass spectrometry under the collaboration with UC Davis WCMC scientists. We believe that this study will provide a significant potential clinical impact because results may lead to clinical methods to increase diagnostic accuracy and an improved understanding of the molecular basis of IC/PBS and its relationship to urologic conditions with overlapping symptoms.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
This West Coast Metabolomics Center sponsored pilot grant goal is to identify and validate interstitial cystitis/painful bladder syndrome (IC/PBS)-associated urinary metabolites. Our central hypothesis is that IC/PBS-associated metabolites in the urine of IC/PBS patients can segregate patients from control subjects, and that their levels are correlated with clinical symptoms. To test this hypothesis, we will identify IC/PBS-associated metabolites in urine using two independent platforms, GC-MS and quadrupole time-of-flight (Q-TOF) mass spectrometry under the collaboration with UC Davis WCMC scientists. We believe that this study will provide a significant potential clinical impact because results may lead to clinical methods to increase diagnostic accuracy and an improved understanding of the molecular basis of IC/PBS and its relationship to urologic conditions with overlapping symptoms.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women
STUDY_SUMMARY
Insulin resistance progressing to type 2 diabetes mellitus (T2DM) is marked by a broad perturbation of macronutrient intermediary metabolism. Understanding the biochemical networks that underlie metabolic homeostasis and how they associate with insulin action will help unravel diabetes etiology and should foster discovery of new biomarkers of disease risk and severity. We examined differences in plasma concentrations of >350 metabolites in fasted obese T2DM vs. obese non-diabetic African-American women, and utilized principal components analysis to identify 158 metabolite components that strongly correlated with fasting HbA1c over a broad range of the latter (r?=??0.631; p<0.0001). In addition to many unidentified small molecules, specific metabolites that were increased significantly in T2DM subjects included certain amino acids and their derivatives (i.e., leucine, 2-ketoisocaproate, valine, cystine, histidine), 2-hydroxybutanoate, long-chain fatty acids, and carbohydrate derivatives. Leucine and valine concentrations rose with increasing HbA1c, and significantly correlated with plasma acetylcarnitine concentrations. It is hypothesized that this reflects a close link between abnormalities in glucose homeostasis, amino acid catabolism, and efficiency of fuel combustion in the tricarboxylic acid (TCA) cycle. It is speculated that a mechanism for potential TCA cycle inefficiency concurrent with insulin resistance is “anaplerotic stress” emanating from reduced amino acid-derived carbon flux to TCA cycle intermediates, which if coupled to perturbation in cataplerosis would lead to net reduction in TCA cycle capacity relative to fuel delivery.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
G/g and g/a are polymorphisms in the promoter region of the UCP3 gene that leads to the gene being enhanced and an increased chance of obesity in those with this polymorphism.
PUBLICATIONS
Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women
Metabolomic profiles in P. gingivalis cells treated with pABA
STUDY_SUMMARY
Many human infections are polymicrobial in origin, and synergistic interactions among community inhabitants control colonization and pathogenic potential (Murray et al., 2014). However, few interspecies interactions have been functionally dissected at the molecular level or characterized on a systems level. Periodontitis, which is the sixth most prevalent infectious disease worldwide (Kassebaum et al., 2014), is associated with a dysbiotic microbial community, and the keystone pathogen Porphyromonas gingivalis forms synergistic communities with the accessory pathogen Streptococcus gordonii (Lamont and Hajishengallis, 2015). P. gingivalis and S. gordonii communicate through co-adhesion and metabolite perception, and close association between P. gingivalis and S. gordonii results in significant changes in the expressed proteomes of both organisms (Kuboniwa et al., 2012, Hendrickson et al., 2012). Here we show that streptococcal 4 aminobenzoate/para-amino benzoic acid (pABA) is required for maximal accumulation of P. gingivalis in communities with S. gordonii. Exogenous pABA upregulates production of fimbrial interspecies adhesins and of a tyrosine phosphorylation-dependent signaling system in P. gingivalis. Consequently, fimbrial-dependent attachment and invasion of epithelial cells by P. gingivalis is also increased by pABA. Moreover, trans-omics studies performed by proteomics and metabolomics showed that pABA induces metabolic shifts within P. gingivalis, predominantly folate derivative biosynthesis. In a murine oral infection model, pABA increased colonization and survival of P. gingivalis, but did not increase virulence. The results establish streptococcal pABA as a major component of the interspecies S. gordonii-P. gingivalis interaction which regulates distinct aspects of polymicrobial synergy.
Study1 Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer (training set)
STUDY_SUMMARY
Recently, the National Lung Cancer Screen Trial (NLST) demonstrated that low-dose CT (LDCT) screening could reduce mortality due to lung cancer by 20%. However, LDCT screening is largely hindered by high false-positive rates (96%), particularly in high-risk populations (heavy smokers), due to the low prevalence rates (less than 2%) of malignant tumors and high incidence of benign lung nodules. Consequently, complementary biomarkers that can be used in conjunction with LDCT screening to improve diagnostic capacities and reduce false-positive rates are highly desirable. Preferably, such complementary tools should be noninvasive and exhibit high sensitivity and specificity. The application of “-omic” sciences (genomics, transcriptomics, proteomics, and metabolomics) represents valuable tools for the discovery and validation of potential biomarkers that can be used for detection of NSCLC. Of these omic sciences, metabolomics has received considerable attention for its application in cancer. Metabolomics is the assessment of small molecules and biochemical intermediates (metabolites) using analytic instrumentation. Metabolites in blood are the product of all cellular processes, which are highly responsive to conditions of disease and environment, and represent the final output products of all organs forming a detailed systemic representation of an individual's current physiologic state. In this study, we used an untargeted metabolomics approach using gas chromatography time-of-flight mass spectrometry (GCTOFMS) to analyze the metabolome of serum and plasma samples both collected from the same patients that were organized into two independent case–control studies (ADC1 and ADC2). In both studies, only NSCLC adenocarcinoma was investigated. The overall objectives were to (i) determine whether individual or combinations of metabolites could be used as a diagnostic test to distinguish NSCLC adenocarcinoma from controls and (ii) to determine which, plasma or serum, provides more accurate classifiers for the detection of lung cancer. We developed individual and multimetabolite classifiers using a training test from the ADC1 study and evaluated the performance of the constructed classifiers, individually or in combination, in an independent test/validation study (ADC2). This study shows the potential of metabolite-based diagnostic tests for detection of lung adenocarcinoma. Further validation in a larger pool of samples is warranted.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control The first set (ADC1) used for biomarker development consisted of serum and plasma samples obtained from 52 stages I–IV NSCLC adenocarcinoma patients (52 plasma and 49 serum), and 31 healthy controls (31 pairs of serum and plasma) for a total of 163 samples. This set was regarded as the training set for biomarker discovery and classifier development. A second, independent case–control study (ADC2) consisting of serum and plasma samples collected from 43 stage I–IV NSCLC adenocarcinoma patients and 43 healthy controls (total 172 samples) was used as an independent test set for biomarker evaluation. A limitation of this study is the relatively small sample size for each cohort (52 cases, 31 controls for ADC1, and 43 cases and 43 controls for ADC2) because patient variability can be a big factor in smaller studies.
Study 2 Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer (test/validation)
STUDY_SUMMARY
Recently, the National Lung Cancer Screen Trial (NLST) demonstrated that low-dose CT (LDCT) screening could reduce mortality due to lung cancer by 20%. However, LDCT screening is largely hindered by high false-positive rates (96%), particularly in high-risk populations (heavy smokers), due to the low prevalence rates (less than 2%) of malignant tumors and high incidence of benign lung nodules. Consequently, complementary biomarkers that can be used in conjunction with LDCT screening to improve diagnostic capacities and reduce false-positive rates are highly desirable. Preferably, such complementary tools should be noninvasive and exhibit high sensitivity and specificity. The application of “-omic” sciences (genomics, transcriptomics, proteomics, and metabolomics) represents valuable tools for the discovery and validation of potential biomarkers that can be used for detection of NSCLC. Of these omic sciences, metabolomics has received considerable attention for its application in cancer. Metabolomics is the assessment of small molecules and biochemical intermediates (metabolites) using analytic instrumentation. Metabolites in blood are the product of all cellular processes, which are highly responsive to conditions of disease and environment, and represent the final output products of all organs forming a detailed systemic representation of an individual's current physiologic state. In this study, we used an untargeted metabolomics approach using gas chromatography time-of-flight mass spectrometry (GCTOFMS) to analyze the metabolome of serum and plasma samples both collected from the same patients that were organized into two independent case–control studies (ADC1 and ADC2). In both studies, only NSCLC adenocarcinoma was investigated. The overall objectives were to (i) determine whether individual or combinations of metabolites could be used as a diagnostic test to distinguish NSCLC adenocarcinoma from controls and (ii) to determine which, plasma or serum, provides more accurate classifiers for the detection of lung cancer. We developed individual and multimetabolite classifiers using a training test from the ADC1 study and evaluated the performance of the constructed classifiers, individually or in combination, in an independent test/validation study (ADC2). This study shows the potential of metabolite-based diagnostic tests for detection of lung adenocarcinoma. Further validation in a larger pool of samples is warranted.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control The first set (ADC1) used for biomarker development consisted of serum and plasma samples obtained from 52 stages I–IV NSCLC adenocarcinoma patients (52 plasma and 49 serum), and 31 healthy controls (31 pairs of serum and plasma) for a total of 163 samples. This set was regarded as the training set for biomarker discovery and classifier development. A second, independent case–control study (ADC2) consisting of serum and plasma samples collected from 43 stage I–IV NSCLC adenocarcinoma patients and 43 healthy controls (total 172 samples) was used as an independent test set for biomarker evaluation. A limitation of this study is the relatively small sample size for each cohort (52 cases, 31 controls for ADC1, and 43 cases and 43 controls for ADC2) because patient variability can be a big factor in smaller studies.
Changes in the metabalome and lipidome in response to exercise training
STUDY_TYPE
HERITAGE (HEalth, RIsk factors, exercise Training And GEnetics) family study
STUDY_SUMMARY
The overall objective of the Heritage Family Study is to study the role of the genotype in cardiovascular, metabolic, and hormonal responses to aerobic exercise training and the contribution of regular exercise to changes in several cardiovascular disease and diabetes risk factors. The study cohort used in this analysis was derived from the pool of 473 Caucasian subjects (230 male and 243 female) from 99 nuclear families who completed ≥58 of the prescribed 60 exercise-training sessions. Utilizing a subsample of this Caucasian cohort, we selected family members from the Quebec center (N=125) to assess the metabolome and lipidome of circulating plasma under two well-defined environmental conditions, the pre- and post-training conditions.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
Serum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer (part I)
STUDY_SUMMARY
Recent computed tomography (CT) screening trials showed that it is effective for early detection of lung cancer, but were plagued by high false positive rates. Additional blood biomarker tests designed to complement CT screening and reduce false positive rates are highly desirable. In the current study, we expand upon our initial experimental findings as part of the discovery phase by evaluating metabolites in serum from subjects with benign or malignant SPNs using a combined approach of gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and hydrophilic liquid chromatography accurate mass quadrupole time-of-flight mass spectrometry (HILIC-qTOFMS). Furthermore, we evaluated serum collected pre-diagnosis and at-diagnosis of lung cancer in addition to samples obtained post-surgical intervention from subjects with malignant SPNs (post-diagnosis). We hypothesize that our systems biology approach to identify candidate metabolomics biomarkers will ultimately lead to improved early detection of lung cancer and can be used in as a companion blood test to LDCT screening.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Serum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer (part II)
STUDY_SUMMARY
Recent computed tomography (CT) screening trials showed that it is effective for early detection of lung cancer, but were plagued by high false positive rates. Additional blood biomarker tests designed to complement CT screening and reduce false positive rates are highly desirable. In the current study, we expand upon our initial experimental findings as part of the discovery phase by evaluating metabolites in serum from subjects with benign or malignant SPNs using a combined approach of gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and hydrophilic liquid chromatography accurate mass quadrupole time-of-flight mass spectrometry (HILIC-qTOFMS). Furthermore, we evaluated serum collected pre-diagnosis and at-diagnosis of lung cancer in addition to samples obtained post-surgical intervention from subjects with malignant SPNs (post-diagnosis). We hypothesize that our systems biology approach to identify candidate metabolomics biomarkers will ultimately lead to improved early detection of lung cancer and can be used in as a companion blood test to LDCT screening.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma (part I)
STUDY_SUMMARY
Lung cancer has been the leading cause of cancer death in the United States and worldwide for many decades. Low dose spiral computerized tomography (LDCT) is likely to become the first approved screening and early detection test in the upcoming year, but it is plagued by a high false-positive rate. There is a need to develop complementary screening and early detection tools. A blood-based lung cancer signature is an attractive solution. Given that our knowledge of the molecular biology of smoking-induced lung cancer has dramatically increased over the past few years, this approach is plausible. To date, this effort has been focused on the identification of genomic and proteomic signatures with limited success. A broader strategy that incorporates additional cancer traits is needed. It is well recognized that wide coverage of cellular metabolism in cancer could help provide valuable diagnostic biomarkers and potentially identify molecular drivers of tumorigenesis. Recent advances in mass spectrometry have enabled comprehensive metabolomic analyses of lipids, carbohydrates, amino acids, and nucleotides within a variety of biologic matrices. Early evidence from metabolomic investigation of cancer has identified many altered biochemical profiles. However, to date, there have been few investigations of lung cancer, and most studies have looked at blood plasma or were limited by small sample sizes with mixed histologies. In the current investigation, gas chromatography time-offlight mass spectrometry (GC-TOF) was used to measure 462 lipid, carbohydrate, amino acid, organic acid, and nucleotide metabolites in 39 malignant and nonmalignant lung tissue pairs from current or former smokers with early stage adenocarcinoma. This study cohort represents patient characteristics and tumor histology most likely to be detected with LDCT screening. We hypothesize that identification of cancer-induced cellular and tissue level biochemical changes can offer a robust method for identification of candidate circulating biomarkers and improve our understanding of biochemical changes involved in adenocarcinoma tumorigenesis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma (part II)
STUDY_SUMMARY
Lung cancer has been the leading cause of cancer death in the United States and worldwide for many decades. Low dose spiral computerized tomography (LDCT) is likely to become the first approved screening and early detection test in the upcoming year, but it is plagued by a high false-positive rate. There is a need to develop complementary screening and early detection tools. A blood-based lung cancer signature is an attractive solution. Given that our knowledge of the molecular biology of smoking-induced lung cancer has dramatically increased over the past few years, this approach is plausible. To date, this effort has been focused on the identification of genomic and proteomic signatures with limited success. A broader strategy that incorporates additional cancer traits is needed. It is well recognized that wide coverage of cellular metabolism in cancer could help provide valuable diagnostic biomarkers and potentially identify molecular drivers of tumorigenesis. Recent advances in mass spectrometry have enabled comprehensive metabolomic analyses of lipids, carbohydrates, amino acids, and nucleotides within a variety of biologic matrices. Early evidence from metabolomic investigation of cancer has identified many altered biochemical profiles. However, to date, there have been few investigations of lung cancer, and most studies have looked at blood plasma or were limited by small sample sizes with mixed histologies. In the current investigation, gas chromatography time-offlight mass spectrometry (GC-TOF) was used to measure 462 lipid, carbohydrate, amino acid, organic acid, and nucleotide metabolites in 39 malignant and nonmalignant lung tissue pairs from current or former smokers with early stage adenocarcinoma. This study cohort represents patient characteristics and tumor histology most likely to be detected with LDCT screening. We hypothesize that identification of cancer-induced cellular and tissue level biochemical changes can offer a robust method for identification of candidate circulating biomarkers and improve our understanding of biochemical changes involved in adenocarcinoma tumorigenesis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry
STUDY_SUMMARY
Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC) adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05). Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
TOTAL_SUBJECTS
82
NUM_MALES
20
NUM_FEMALES
62
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control
Long-Chain Fatty Acid Combustion Rate Is Associated with Unique Metabolite Profiles in Skeletal Muscle Mitochondria
STUDY_SUMMARY
Incomplete or limited long-chain fatty acid (LCFA) combustion in skeletal muscle has been associated with insulin resistance. Signals that are responsive to shifts in LCFA β-oxidation rate or degree of intramitochondrial catabolism are hypothesized to regulate second messenger systems downstream of the insulin receptor. Recent evidence supports a causal link between mitochondrial LCFA combustion in skeletal muscle and insulin resistance. We have used unbiased metabolite profiling of mouse muscle mitochondria with the aim of identifying candidate metabolites within or effluxed from mitochondria and that are shifted with LCFA combustion rate. This proof-of-principle study establishes that large-scale metabolomics methods can be applied to organelle-level models to discover metabolite patterns reflective of LCFA combustion, which may lead to identification of molecules linking muscle fat metabolism and insulin signaling. Our results suggest that future studies should focus on the fate of effluxed TCA cycle intermediates and on mechanisms ensuring their replenishment during LCFA metabolism in skeletal muscle.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
The circadian oscillator in Synechococcus elongatus controls metabolite partitioning during diurnal growth
STUDY_SUMMARY
Cyanobacteria are increasingly being considered for use in large-scale outdoor production of fuels and industrial chemicals. Cyanobacteria can anticipate daily changes in light availability using an internal circadian clock and rapidly alter their metabolic processes in response to changes light availability. Understanding how signals from the internal circadian clock and external light availability are integrated to control metabolic shifts will be important for engineering cyanobacteria for production in natural outdoor environments. This study has assessed how “knowing” the correct time of day, via the circadian clock, affects metabolic changes when a cyanobacterium goes through a dark-to-light transition. Our data show that the circadian clock plays an important role in inhibiting activation of the oxidative pentose phosphate pathway in the morning. Synechococcus elongatus PCC 7942 is a genetically tractable model cyanobacterium that has been engineered to produce industrially relevant biomolecules and is the best-studied model for a prokaryotic circadian clock. However, the organism is commonly grown in continuous light in the laboratory, and data on metabolic processes under diurnal conditions are lacking. Moreover, the influence of the circadian clock on diurnal metabolism has been investigated only briefly. Here, we demonstrate that the circadian oscillator influences rhythms of metabolism during diurnal growth, even though light–dark cycles can drive metabolic rhythms independently. Moreover, the phenotype associated with loss of the core oscillator protein, KaiC, is distinct from that caused by absence of the circadian output transcriptional regulator, RpaA (regulator of phycobilisome-associated A). Although RpaA activity is important for carbon degradation at night, KaiC is dispensable for those processes. Untargeted metabolomics analysis and glycogen kinetics suggest that functional KaiC is important for metabolite partitioning in the morning. Additionally, output from the oscillator functions to inhibit RpaA activity in the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active output state, phenocopies a ΔrpaA strain. Inhibition of RpaA by the oscillator in the morning suppresses metabolic processes that normally are active at night, and kaiC-null strains show indications of oxidative pentose phosphate pathway activation as well as increased abundance of primary metabolites. Inhibitory clock output may serve to allow secondary metabolite biosynthesis in the morning, and some metabolites resulting from these processes may feed back to reinforce clock timing.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
The first 4 samples were a test run to see how efficient the analysis was and were run on a lipidomics platform. The next 12 samples were the used in the paper and were the same as the original 4 samples, but they were split into 3 biological replicates and run on the GC platform.
The circadian oscillator in Synechococcus elongatus controls metabolite partitioning during diurnal growth (part II)
STUDY_SUMMARY
Cyanobacteria are increasingly being considered for use in large-scale outdoor production of fuels and industrial chemicals. Cyanobacteria can anticipate daily changes in light availability using an internal circadian clock and rapidly alter their metabolic processes in response to changes light availability. Understanding how signals from the internal circadian clock and external light availability are integrated to control metabolic shifts will be important for engineering cyanobacteria for production in natural outdoor environments. This study has assessed how “knowing” the correct time of day, via the circadian clock, affects metabolic changes when a cyanobacterium goes through a dark-to-light transition. Our data show that the circadian clock plays an important role in inhibiting activation of the oxidative pentose phosphate pathway in the morning. Synechococcus elongatus PCC 7942 is a genetically tractable model cyanobacterium that has been engineered to produce industrially relevant biomolecules and is the best-studied model for a prokaryotic circadian clock. However, the organism is commonly grown in continuous light in the laboratory, and data on metabolic processes under diurnal conditions are lacking. Moreover, the influence of the circadian clock on diurnal metabolism has been investigated only briefly. Here, we demonstrate that the circadian oscillator influences rhythms of metabolism during diurnal growth, even though light–dark cycles can drive metabolic rhythms independently. Moreover, the phenotype associated with loss of the core oscillator protein, KaiC, is distinct from that caused by absence of the circadian output transcriptional regulator, RpaA (regulator of phycobilisome-associated A). Although RpaA activity is important for carbon degradation at night, KaiC is dispensable for those processes. Untargeted metabolomics analysis and glycogen kinetics suggest that functional KaiC is important for metabolite partitioning in the morning. Additionally, output from the oscillator functions to inhibit RpaA activity in the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active output state, phenocopies a ΔrpaA strain. Inhibition of RpaA by the oscillator in the morning suppresses metabolic processes that normally are active at night, and kaiC-null strains show indications of oxidative pentose phosphate pathway activation as well as increased abundance of primary metabolites. Inhibitory clock output may serve to allow secondary metabolite biosynthesis in the morning, and some metabolites resulting from these processes may feed back to reinforce clock timing.
INSTITUTE
UC Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
The first 4 samples were a test run to see how efficient the analysis was and were run on a lipidomics platform. The next 12 samples were the used in the paper and were the same as the original 4 samples, but they were split into 3 biological replicates and run on the GC platform.
Recently, major efforts have been directed toward early detection of lung cancer through low-dose computed tomography (LDCT) scanning. Data from the National Lung Screening Trial (NLST) suggest that yearly screening with thoracic LDCT scanning for high-risk current and former smokers reduces lung cancer mortality by 20% and total mortality by 7%. However, issues including indeterminate nodules detected by LDCT and radiation exposure impact the practicality of LDCT-based screening on a national and global basis. A blood-based biomarker or multiplexed marker panel that could complement LDCT would represent a major advance in implementing lung cancer screening. Efforts to develop blood-based biomarkers for lung cancer early detection using a variety of methodologies are currently ongoing. Proteomic studies have led to the identification of several candidate markers including pro-surfactantproteinB(pro-SFTPB), a target of a lineage-survival oncogene in lung cancer, NKX2-1.Validation studies using blood samples collected at the time of LDCT screening for lung cancer substantiated the performance of pro-SFTPB. Multivariable logistic regression models were used to evaluate the predictive ability of pro-SFTPB. The area under the curve (AUC) values of the full model with and without pro-SFTPB were 0.741 (95% CI, 0.696 to 0.783) and 0.669 (95%CI, 0.620 to 0.717), respectively (difference in AUC, P_.001). Single markers are unlikely to have sufficient performance for implementation in a screening setting, hence the need to explore several discovery platforms to identify markers that provide complementary performance. Metabolomics represents a global unbiased approach to the profiling of small molecules and has been established as a platform for biomarker discovery for a variety of human biofluids and tissues. Here we used an untargeted liquid chromatography/mass spectrometry (MS) metabolomics approach to identify metabolites that distinguish human sera collected before the diagnosis of lung cancer from matched control sera in a prospective cohort of highrisk patients from the Beta-Carotene and Retinol Efficacy Trial (CARET).
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Long-term neural and physiological phenotyping of a single human
STUDY_TYPE
Longitudinal
STUDY_SUMMARY
The dynamics of human brain function are increasingly well understood at the short timescale of seconds/minutes (for example, through studies of learning) and the long timescale of years/decades (for example, through studies of development andageing), but almost nothing is known about how the human brainfunction varies across the range of days to months. This is a critical gap, because major psychiatric disorders show large fluctuations in brain function over this timescale. However, the kind of dense longitudinal phenotyping that is necessary to understand this question is extremely challenging with healthy human volunteers,who are unlikely to be sufficiently motivated to sustain frequent participation in a study over a long period. For this reason, the participation of motivated experimenters can be uniquely useful for demanding longitudinal studies. We investigated the long-range dynamics of brain function andtheir relation to a broad set of psychological and biological variables in a single healthy human (author R.A.P.) over the course of 532 days (along with several follow-up visits), representing one of the most intensive biological characterizations of a single individual ever performed (referred to hereafter as the MyConnectomestudy). The study was designed to measure the broadest possible range of human phenotypes (the phenome’3,4) to allow the widespread assessment of relations between psychological, neural and metabolic function. The results of the present study demonstrate that healthy brain function shows rich dynamics over the course of 18 months, and that these dynamics are paralleled by ongoing fluctuations in psychological and physiological function as observed in behaviour,gene expression and metabolomic measurements. These findings provide a proof of concept for the dynamic longitudinal phenotyping of individuals, which we propose will be crucial togain a better understanding of the substantial fluctuations in psychological and neural function in individuals with major psychiatric disorders.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
E.coli effects on growth and substrate uptake of green algae (part I - HILIC)
STUDY_SUMMARY
The purpose of this project was to quantify the exchange of thiamine between bacteria and algae. We previously observed that the model bacteria, Escherichia coli, enhanced the growth and substrate uptake of the green algae, Auxenochlorella protothecoides. We hypothesized that this growth enhancement was due to the secretion of thiamine derivatives or degradation products by E. coli followed by uptake of these compounds by A. protothecoides. Targeted and untargeted LCMS revealed the presence of thiamine dervatives in E. coli cell extracts. These LCMS methods were also used to quantify thiamine derivatives and two degradation products, HMP and THZ, present in E. coli medium after cell removal. The LCMS results along with culture studies were employed to show that thiamine derivatives and degradation products were the primary mechanism of symbiosis between E. coli and A. protothecoides.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
E.coli effects on growth and substrate uptake of green algae (part II - Reverse Phase)
STUDY_SUMMARY
The purpose of this project was to quantify the exchange of thiamine between bacteria and algae. We previously observed that the model bacteria, Escherichia coli, enhanced the growth and substrate uptake of the green algae, Auxenochlorella protothecoides. We hypothesized that this growth enhancement was due to the secretion of thiamine derivatives or degradation products by E. coli followed by uptake of these compounds by A. protothecoides. Targeted and untargeted LCMS revealed the presence of thiamine dervatives in E. coli cell extracts. These LCMS methods were also used to quantify thiamine derivatives and two degradation products, HMP and THZ, present in E. coli medium after cell removal. The LCMS results along with culture studies were employed to show that thiamine derivatives and degradation products were the primary mechanism of symbiosis between E. coli and A. protothecoides.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
Inhibition of diamine oxidase promotes uptake of putrescine from rat small intestine
STUDY_SUMMARY
Metformin, a biguanide molecule, which is used as first line therapy for type 2 diabetes. In this study, we would like to investigate the inhibition of an enzyme called diamine oxidase (DAO) (also known as ABP1), by metformin. Based on our preliminary in vitro study using diamine oxidase enzyme, we saw increased level of putrescine with increasing metformin concentrations (see reference PMID: 26335661). This proposed in vivo study was to determine whether metformin could increase putrescine levels and other metabolites in mice. Aminoguanidine, a known inhibitor of DAO, in this study as positive control, following similar study design described in this paper (PMID: 8912017).
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Impact of glucose on the central metabolome of C. minutissima
STUDY_SUMMARY
Axenic Chlorella minutissima (UTEX 2341) was grown under mixotrophic and autotrophic conditions to compare metabolome differences. The purpose of this study was to understand how glucose impacted the central metabolome of C. minutissima.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
The proton channel HVCN1 is expressed in B cell malignancies at high levels but its role remains unclear. From initial experiments during which HVCN1 was downregulated in human multiple myeloma cell lines, we observed an increase in some glycolytic and TCA metabolites. We want to get a better idea if HVCN1 is playing a role in regulating energy metabolism in multiple myeloma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic Profiling in Early Pregnancy using Pre-Diagnostic Sera from Women Who Developed Placental Abruption
STUDY_TYPE
Metabolomics Biocrates Panel
STUDY_SUMMARY
Placental abruption (PA) is an ischemic placental disorder that results from the premature separation of the placenta from the wall of the uterus before delivery of the fetus. This disorder is associated with pre-term delivery, fetal death, maternal hemorrhagic shock, and renal failure. Several physiologic disturbances, such as oxidative stress, carbohydrate/fatty acid metabolism, and mitochondrial dysfunction, have been associated with ischemic placental disorder as well as with placental abruption. This preliminary study proposes to identify metabolites associated with incident placental abruption using existing serum and clinical data from a previously studied cohort. Metabolomics analysis will be carried out on maternal serum (51 cases and 51 controls) collected in early pregnancy (early second trimester).
INSTITUTE
Harvard School of Public Health
DEPARTMENT
Swedish Medical Center
LAST_NAME
Wlliams
FIRST_NAME
Michelle
ADDRESS
677 Huntington Ave. Kresge Room 905A, Boston, MA 02446
Metabolic profiling during ex vivo machine perfusion of the human liver
STUDY_SUMMARY
As donor organ shortages persist, functional machine perfusion is under investigation to improve preservation of the donor liver. The transplantation of donation after circulatory death (DCD) livers is limited by poor outcomes, but its application may be expanded by ex vivo repair and assessment of the organ before transplantation. Here we employed subnormothermic (21 °C) machine perfusion of discarded human livers combined with metabolomics to gain insight into metabolic recovery during machine perfusion. Improvements in energetic cofactors and redox shifts were observed, as well as reversal of ischemia-induced alterations in selected pathways, including lactate metabolism and increased TCA cycle intermediates. We next evaluated whether DCD livers with steatotic and severe ischemic injury could be discriminated from ‘transplantable’ DCD livers. Metabolomic profiling was able to cluster livers with similar metabolic patterns based on the degree of injury. Moreover, perfusion parameters combined with differences in metabolic factors suggest variable mechanisms that result in poor energy recovery in injured livers. We conclude that machine perfusion combined with metabolomics has significant potential as a clinical instrument for the assessment of preserved livers.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolic profiling during ex vivo machine perfusion of the human liver (part III)
STUDY_SUMMARY
As donor organ shortages persist, functional machine perfusion is under investigation to improve preservation of the donor liver. The transplantation of donation after circulatory death (DCD) livers is limited by poor outcomes, but its application may be expanded by ex vivo repair and assessment of the organ before transplantation. Here we employed subnormothermic (21 °C) machine perfusion of discarded human livers combined with metabolomics to gain insight into metabolic recovery during machine perfusion. Improvements in energetic cofactors and redox shifts were observed, as well as reversal of ischemia-induced alterations in selected pathways, including lactate metabolism and increased TCA cycle intermediates. We next evaluated whether DCD livers with steatotic and severe ischemic injury could be discriminated from ‘transplantable’ DCD livers. Metabolomic profiling was able to cluster livers with similar metabolic patterns based on the degree of injury. Moreover, perfusion parameters combined with differences in metabolic factors suggest variable mechanisms that result in poor energy recovery in injured livers. We conclude that machine perfusion combined with metabolomics has significant potential as a clinical instrument for the assessment of preserved livers.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
The first 4 samples were a test run to see how efficient the analysis was and were run on a lipidomics platform. The next 12 samples were the used in the paper and were the same as the original 4 samples, but they were split into 3 biological replicates and run on the GC platform.
Toxicokinetics and Metabolomic Disrupting of the Flame Retardant Mixture Firemaster 550
STUDY_TYPE
Low Dose and High Dose Exposure to Firemaster (FM) 550
STUDY_SUMMARY
Pregnant lab rats (dams) were assigned to three groups: a control group, which was not exposed to Firemaster (FM) 550; a low-dose group, which ingested 100 µg of FM550 once daily throughout pregnancy; and a high-dose group, which ingested 1000 µg FM550 on the same schedule. The placentas were harvested immediately after birth, frozen on dry ice and pulverized in liquid nitrogen via mortar and pestle. The overall objective is to investigate the differences in the metabolic profiles of the placentas in each phenotypic group.
INSTITUTE
RTI International
DEPARTMENT
RCMRC
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E Cornwallis Road, Research Triangle Park, NC 27709
Controlled Human Exposure to Particulate Matter (PM) and Gaseous Co-Pollutants
STUDY_TYPE
Exposome Evaluation
STUDY_SUMMARY
This study is designed to provide the environmental aspects to support both the acquisition of study samples and the advancement of environmental chemical speciation information and data analyis needed. The aims of the study are as follows:1)Do the metabolomics profiles appear to be impacted by exposure to PM and NO2+PM. 2)are the metabolomic profiles related to the PM and NO2+PM distinct 3)which features (chemical or physical) of the PM and NO2+PM have the most significant impact on the metabolomic profiles.
INSTITUTE
RTI International
DEPARTMENT
RCMRC
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E Cornwallis Road, Research Triangle Park, NC, 27519, USA
The role of CFTR in the regulation of intrinsic defense mechanisms of exocrine secretions
STUDY_SUMMARY
This study was designed as a pilot to determine if the concentrations of selected ions in salivary gland secretions were influenced by the absence of CFTR on the apical surfaces of glandular cells and ductal epithelia. To this end, five cystic fibrosis children homozygous for Phe508 were to be recruited with their heterozygous non-CF mothers. For adaptation and development of the assays to a microtiter format, saliva samples were collected from non-CF control subjects initially to optimize the assays recognizing that the volumes for analyses would be small. The values obtained with these non-CF control samples were also compared to that of the homozygous and heterozygous CF subjects. As residual volume permits, these samples will be further analyzed for metabolic constituent profiles.
INSTITUTE
RTI International
DEPARTMENT
RCMRC
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E Cornwallis Road, Research Triangle Park, NC 27709
Impact Of High Sugar Diet On L-Arginine Metabolism In The Lung
STUDY_SUMMARY
Asthma is a progressive inflammatory airways disease that leads to structural airway changes and debilitating symptoms in many severely affected adults. We need novel therapeutic agents that are affordable, can decrease the reliance on steroids, and can improve quality of life. This clinical and mechanistic study has the potential to impact treatment of a subset of adult severe asthmatics and to further our understanding of the mechanisms of L-arginine metabolism and NO biology in the airways of asthmatics. We will pursue a clinical trial in subjects not well controlled on standard drug therapy; this strategy will address whether L-arginine is efficacious in patients receiving standard of care medications. In studies using animal models, we and others have shown that interventions that augment NO levels, through either supplementation of L-arginine or inhibition of arginase, decrease allergic airway inflammation and hyperresponsiveness-the two hallmarks of asthma. Overall, we hypothesize that a responder subset of adult severe asthma patients will derive clinical benefit from supplemental L-arginine therapy and that these patients will have a lower exhaled NO concentrations (<20 ppb) and a higher NOS2/Arg1 mRNA and protein ratio in their airway epithelial cells than non-responders. We aim to: 1) test the hypothesis that uncontrolled, adult severe asthma patients with exhaled breath NO concentrations <20 ppb will have fewer asthma exacerbations over 3 months when treated with L-arginine compared to patients with FeNO > 25, 2) determine the mechanisms by which L-arginine affects the regulation of NOS and arginase enzymes in primary airway epithelial cell cultures from severe asthmatic subjects, and 3) test the hypothesis that inhaled nanoparticle carrier formulations of L-arginine will decrease airway inflammation, airway hyperresponsiveness, and airway fibrosis at lower doses than systemically administered L-arginine. The major impact of our study will be to identify the adult severe asthma cohort that will benefit from supplemental L-arginine therapy. Our ultimate goal is to develop novel therapeutic agents to treat adult severe asthma patients better. PUBLIC HEALTH RELEVANCE: Asthma is a progressive inflammatory airways disease that leads to structural airway changes and debilitating symptoms in many severely affected adults. This clinical study has the potential to improve the care of adult severe asthmatics and to further our understanding of the mechanisms of L-arginine metabolism and nitric oxide biology in the lung. If we demonstrate that L-arginine supplementation can decrease asthma attacks in a subset of severe asthmatics, it will have great implications for future research as well as for the daily lives of patients with asthma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
ms3076 T1D poor glycemic control and control samples
STUDY_TYPE
Plasma metabolites in T1 diabetes
STUDY_SUMMARY
The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Type 1 Diabetes good glycemic control and controls samples
STUDY_TYPE
Plasma metabolites in T1 diabetes
STUDY_SUMMARY
The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Differences in mycoplasma growth due to different mediums
STUDY_SUMMARY
The object is to learn if there are variations in the lipid profiles of the three genomic variants (relative to one another) and if there are difference the lipid profiles due to growth in medium having different supplements. Mycoplasmas are eubacteria, but have only a single plasma membrane and no cell wall. They acquire FAs and cholesterol and other (perhaps many unknown) lipids from the medium which is complex and contains mammalian serum. Various mycoplasma species have been shown to contain a wide spectrum of bacterial lipids, but the composition is unknown for this mycoplasma species. We are particularly interested in ratios of membrane lipids among our strains, in part to gain clues about differences in metabolic pathways pertinent to membrane biogenesis; and to predict any underlying features that could relate to the extremely different modes of cell propagation observed among these genomic constructs.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomics Approach to Allograft Assessment in Liver Transplantation
STUDY_TYPE
Retrospective analysis of biobanked liver tissue from organ donors
STUDY_SUMMARY
This pilot study is designed to apply several types of metabolomic analysis for liver allograft assessment with the aim of identifying candidate biomarkers for allograft function and to develop a methodology that could be applied to larger scale studies. The three main categories of metabolomic analysis are reflected in each of the specific aims, including a targeted profiling of central carbon metabolism, open lipidomic and metabolomic profiling for hypothesis generation and MALDI-IMS for tissue-based spatial analysis. Each of these approaches offers potential benefits that could be optimized in a protocol for larger scale studies depending the results of the pilot investigations.
Non targeted metabolomics of gastrocnemius tissue samples obtained from 20 month old (old) mice- Both Sham and after inducing lung injury
STUDY_TYPE
Non targeted metabolomic analysis
STUDY_SUMMARY
Introduction: Older patients are more likely to acquire and die from acute respiratory distress syndrome (ARDS) and muscle weakness may be more significant in older survivors. Recent data implicate muscle ring finger protein 1 (MuRF1) in lung injury-induced skeletal muscle atrophy in young mice and identify an alternative role for MuRF1 in cardiac metabolism regulation through inhibition of fatty acid oxidation. Objectives: To develop a model of lung injury-induced muscle wasting in old mice and to evaluate the skeletal muscle metabolomic profile of adult and old acute lung injury (ALI) mice. Methods: Young (2 month), adult (6 month) and old (20 month) male C57Bl6J mice underwent Sham (intratracheal H2O) or ALI [intratracheal E. coli lipopolysaccharide (i.t. LPS)] conditions and muscle functional testing. Metabolomic analysis on gastrocnemius muscle was performed using gas chromatography-mass spectrometry (GC-MS). Results: Old ALI mice had increased mortality and failed to recover skeletal muscle function compared to adult ALI mice. Muscle MuRF1 expression was increased in old ALI mice at day 3. Non-targeted muscle metabolomics revealed alterations in amino acid biosynthesis and fatty acid metabolism in old ALI mice. Targeted metabolomics of fatty acid intermediates (acyl-carnitines) and amino acids revealed a reduction in long chain acyl-carnitines in old ALI mice. Conclusion: This study demonstrates age-associated susceptibility to ALI-induced muscle wasting which parallels a metabolomic profile suggestive of altered muscle fatty acid metabolism. MuRF1 activation may contribute to both atrophy and impaired fatty acid oxidation, which may synergistically impair muscle function in old ALI mice.
INSTITUTE
University of North Carolina, Duke University
DEPARTMENT
UNC McAllister Heart Institute, Duke Molecular Physiology Institute
LABORATORY
Multiple Centers
LAST_NAME
Willis, Ilaiwy
FIRST_NAME
Monte, Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Non targeted metabolomics of gastrocnemius tissue samples obtained from 6 month old (adult) mice- Both Sham and after inducing lung injury
STUDY_TYPE
Non targeted metabolomic analysis
STUDY_SUMMARY
Introduction: Older patients are more likely to acquire and die from acute respiratory distress syndrome (ARDS) and muscle weakness may be more significant in older survivors. Recent data implicate muscle ring finger protein 1 (MuRF1) in lung injury-induced skeletal muscle atrophy in young mice and identify an alternative role for MuRF1 in cardiac metabolism regulation through inhibition of fatty acid oxidation. Objectives: To develop a model of lung injury-induced muscle wasting in old mice and to evaluate the skeletal muscle metabolomic profile of adult and old acute lung injury (ALI) mice. Methods: Young (2 month), adult (6 month) and old (20 month) male C57Bl6J mice underwent Sham (intratracheal H2O) or ALI [intratracheal E. coli lipopolysaccharide (i.t. LPS)] conditions and muscle functional testing. Metabolomic analysis on gastrocnemius muscle was performed using gas chromatography-mass spectrometry (GC-MS). Results: Old ALI mice had increased mortality and failed to recover skeletal muscle function compared to adult ALI mice. Muscle MuRF1 expression was increased in old ALI mice at day 3. Non-targeted muscle metabolomics revealed alterations in amino acid biosynthesis and fatty acid metabolism in old ALI mice. Targeted metabolomics of fatty acid intermediates (acyl-carnitines) and amino acids revealed a reduction in long chain acyl-carnitines in old ALI mice. Conclusion: This study demonstrates age-associated susceptibility to ALI-induced muscle wasting which parallels a metabolomic profile suggestive of altered muscle fatty acid metabolism. MuRF1 activation may contribute to both atrophy and impaired fatty acid oxidation, which may synergistically impair muscle function in old ALI mice.
INSTITUTE
University of North Carolina, Duke University
DEPARTMENT
UNC McAllister Heart Institute, Duke Molecular Physiology Institute
LABORATORY
Multiple Centers
LAST_NAME
Willis, Ilaiwy
FIRST_NAME
Monte, Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
targeted metabolomics of gastrocnemius tissue samples obtained from 6 month old (adult) mice- Both Sham and after inducing lung injury
STUDY_TYPE
targeted metabolomic analysis
STUDY_SUMMARY
Introduction: Older patients are more likely to acquire and die from acute respiratory distress syndrome (ARDS) and muscle weakness may be more significant in older survivors. Recent data implicate muscle ring finger protein 1 (MuRF1) in lung injury-induced skeletal muscle atrophy in young mice and identify an alternative role for MuRF1 in cardiac metabolism regulation through inhibition of fatty acid oxidation. Objectives: To develop a model of lung injury-induced muscle wasting in old mice and to evaluate the skeletal muscle metabolomic profile of adult and old acute lung injury (ALI) mice. Methods: Young (2 month), adult (6 month) and old (20 month) male C57Bl6J mice underwent Sham (intratracheal H2O) or ALI [intratracheal E. coli lipopolysaccharide (i.t. LPS)] conditions and muscle functional testing. Metabolomic analysis on gastrocnemius muscle was performed using gas chromatography-mass spectrometry (GC-MS). Results: Old ALI mice had increased mortality and failed to recover skeletal muscle function compared to adult ALI mice. Muscle MuRF1 expression was increased in old ALI mice at day 3. Non-targeted muscle metabolomics revealed alterations in amino acid biosynthesis and fatty acid metabolism in old ALI mice. Targeted metabolomics of fatty acid intermediates (acyl-carnitines) and amino acids revealed a reduction in long chain acyl-carnitines in old ALI mice. Conclusion: This study demonstrates age-associated susceptibility to ALI-induced muscle wasting which parallels a metabolomic profile suggestive of altered muscle fatty acid metabolism. MuRF1 activation may contribute to both atrophy and impaired fatty acid oxidation, which may synergistically impair muscle function in old ALI mice.
INSTITUTE
University of North Carolina, Duke University
DEPARTMENT
UNC McAllister Heart Institute, Duke Molecular Physiology Institute
LABORATORY
Multiple Centers
LAST_NAME
Willis, Ilaiwy
FIRST_NAME
Monte, Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Targeted metabolomics of gastrocnemius tissue samples obtained from 20 month old (old) mice- Both Sham and after inducing lung injury (part II)
STUDY_TYPE
Targeted metabolomic analysis
STUDY_SUMMARY
Introduction: Older patients are more likely to acquire and die from acute respiratory distress syndrome (ARDS) and muscle weakness may be more significant in older survivors. Recent data implicate muscle ring finger protein 1 (MuRF1) in lung injury-induced skeletal muscle atrophy in young mice and identify an alternative role for MuRF1 in cardiac metabolism regulation through inhibition of fatty acid oxidation. Objectives: To develop a model of lung injury-induced muscle wasting in old mice and to evaluate the skeletal muscle metabolomic profile of adult and old acute lung injury (ALI) mice. Methods: Young (2 month), adult (6 month) and old (20 month) male C57Bl6J mice underwent Sham (intratracheal H2O) or ALI [intratracheal E. coli lipopolysaccharide (i.t. LPS)] conditions and muscle functional testing. Metabolomic analysis on gastrocnemius muscle was performed using gas chromatography-mass spectrometry (GC-MS). Results: Old ALI mice had increased mortality and failed to recover skeletal muscle function compared to adult ALI mice. Muscle MuRF1 expression was increased in old ALI mice at day 3. Non-targeted muscle metabolomics revealed alterations in amino acid biosynthesis and fatty acid metabolism in old ALI mice. Targeted metabolomics of fatty acid intermediates (acyl-carnitines) and amino acids revealed a reduction in long chain acyl-carnitines in old ALI mice. Conclusion: This study demonstrates age-associated susceptibility to ALI-induced muscle wasting which parallels a metabolomic profile suggestive of altered muscle fatty acid metabolism. MuRF1 activation may contribute to both atrophy and impaired fatty acid oxidation, which may synergistically impair muscle function in old ALI mice.
INSTITUTE
University of North Carolina, Duke University
DEPARTMENT
UNC McAllister Heart Institute, Duke Molecular Physiology Institute
LABORATORY
Multiple Centers
LAST_NAME
Willis, Ilaiwy
FIRST_NAME
Monte, Amro
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Targeted metabolomics of MuRF1 overexpressing cardiomyocytes compared to their wildtype controls (part I)
STUDY_TYPE
Targeted metabolomic analysis
STUDY_SUMMARY
The transcriptional regulation of peroxisome proliferator-activated receptor (PPAR) a by post-translational modification, such as ubiquitin, has not been described. We report here for the first time an ubiquitin ligase (muscle ring finger-1/MuRF1) that inhibits fatty acid oxidation by inhibiting PPARa, but not PPARß/d or PPAR? in cardiomyocytes in vitro. Similarly, MuRF1 Tg+ hearts showed significant decreases in nuclear PPARa activity and acyl-carnitine intermediates, while MuRF1-/- hearts exhibited increased PPARa activity and acyl-carnitine intermediates. MuRF1 directly interacts with PPARa, mono-ubiquitinates it, and targets it for nuclear export to inhibit fatty acid oxidation in a proteasome independent manner. We then identified a previously undescribed nuclear export sequence in PPARa, along with three specific lysines (292, 310, 388) required for MuRF1's targeting of nuclear export. These studies identify the role of ubiquitination in regulating cardiac PPARa, including the ubiquitin ligase that may be responsible for this critical regulation of cardiac metabolism in heart failure.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister Heart Institute, Department of Internal Medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Targeted metabolomics of MuRF1 Knockdown cardiomyocytes compared to their wildtype controls (part 2)
STUDY_TYPE
Targeted metabolomic analysis
STUDY_SUMMARY
The transcriptional regulation of peroxisome proliferator-activated receptor (PPAR) α by post-translational modification, such as ubiquitin, has not been described. We report here for the first time an ubiquitin ligase (muscle ring finger-1/MuRF1) that inhibits fatty acid oxidation by inhibiting PPARα, but not PPARβ/δ or PPARγ in cardiomyocytes in vitro. Similarly, MuRF1 Tg+ hearts showed significant decreases in nuclear PPARα activity and acyl-carnitine intermediates, while MuRF1−/− hearts exhibited increased PPARα activity and acyl-carnitine intermediates. MuRF1 directly interacts with PPARα, mono-ubiquitinates it, and targets it for nuclear export to inhibit fatty acid oxidation in a proteasome independent manner. We then identified a previously undescribed nuclear export sequence in PPARα, along with three specific lysines (292, 310, 388) required for MuRF1s targeting of nuclear export. These studies identify the role of ubiquitination in regulating cardiac PPARα, including the ubiquitin ligase that may be responsible for this critical regulation of cardiac metabolism in heart failure.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister Heart Institute, Department of Internal Medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
C2C12 stretch cessation models muscle atrophy and anaplerotic changes in metabolism
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
Studies of skeletal muscle disuse either in patients on bed rest or experimentally in animals(immobilization) have demonstrated that decreased protein synthesis is common, with transient parallel increases in protein degradation. Muscle disuse atrophy involves a process of transition from slow to fast myosin fiber types 6 . A shift toward glycolysis, decreased capacity for fat oxidation, and substrate accumulation in atrophied muscles have been reported as has accommodation of the liver with an increased gluconeogenic capacity. Recent studies have modeled skeletal muscle disuse by using cyclic stretch of differentiated myotubes (C2C12), which mimics the loading pattern of mature skeletal muscle, followed by cessation of stretch.We utilized this model to determine the metabolic changes using non-targeted metabolomics analysis of the media. We identified increases in amino acids resulting from protein degradation (largely sarcomere) that occurs with muscle atrophy that are involved in feeding the Kreb’s cycle through anaplerosis. Specifically, we identified increased alanine/proline metabolism (significantly elevated proline, alanine, glutamine, and asparagine) and increased -ketoglutaric acid, the proposed Kreb’s cycle intermediate being fed by the alanine/proline metabolic anaplerotic mechanism. Additionally, several unique pathways not clearly delineated in previous studies of muscle unloading were seen, including: 1) elevated ethanolamine and elevated keto-acids (e.g. 2-ketoleucine and 2-keovaline) represent intermediates in the Ehlrich amino acid degradation pathway, which feeds into a metabolic pathway supplying acetyl-CoA and 2-hydroxybutyrate (also significantly increased); and 2) elevated guanine, an intermediate of purine metabolism, was seen at 12 hours unloading. Given the interest in targeting different aspects of the ubiquitin proteasome system to inhibit protein degradation, this C2C12 system may allow the identification of direct and indirect alterations in metabolism due to anaplerosis or through other yet to be identified mechanisms using a non-targeted metabolomics approach.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister Heart Institute
LABORATORY
Mutliple Centers
LAST_NAME
Ilaiwy, WIllis
FIRST_NAME
Amro, Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Quantitative measurements of vitamin D in T1D poor control, good control, and controls.
STUDY_TYPE
Quantitative measurements of vitamin D
STUDY_SUMMARY
The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Plasma sphingolipid changes with autopsy-confirmed Lewy body or Alzheimer's pathology
STUDY_TYPE
targeted sphingolipid and fatty acid analyses
STUDY_SUMMARY
We identified four groups with available plasma 2 years before death: high (n = 12) and intermediate-likelihood DLB (n = 14) based on the third report of the DLB consortium; dementia with Alzheimer's pathology (AD; n = 18); and cognitively normal with normal aging pathology (n = 21). Lipids were measured using ESI/MS/MS.
Quantitative measurements of free fatty acid in T1D poor control, good control, and controls.
STUDY_TYPE
Quantitative measurements of free fatty acid
STUDY_SUMMARY
The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Quantitative measurements of amino acids in T1D poor control, good control, and controls.
STUDY_TYPE
Quantitative measurements of amino acid
STUDY_SUMMARY
The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Metabolomic Profiling of the Malaria Box Reveals Antimalarial Target Pathways
STUDY_SUMMARY
Here we interrogated the in vitro metabolic effects of 189 drugs (including 169 of the drug-like compounds from the Malaria Box) using ultra-high performance liquid chromatography mass-spectrometry (UHPLC-MS). The resulting metabolic fingerprints provide information on the parasite biochemical pathways affected by pharmacologic intervention and offer a critical blueprint for selecting and advancing lead compounds as next-generation antimalarial drugs. Our results reveal several major classes of metabolic disruption, which allow us to predict the mode-of-action (MoA) for many of the Malaria Box compounds.
INSTITUTE
Penn State University
LAST_NAME
Llinas
FIRST_NAME
Manuel
ADDRESS
W126 Millenium Science Complex, University Park, PA 16802
Quantitative measurements of TCA cycle metabolites in T1D poor control, good control, and controls.
STUDY_TYPE
Quantitative measurements of plasma levels of tricarboxylic acid (TCA) cycle metabolites
STUDY_SUMMARY
The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.
Preconcentration of organic solutes in urine by bubble bursting
STUDY_TYPE
Sample preparation for MS analysis
STUDY_SUMMARY
The chemical sensitivity of urine metabolomics analysis is greatly compromised due to the large amounts of inorganic salts in urine (NaCl, KCl), which are detrimental to analytical instrumentation, e.g. chromatographic columns or mass spectrometers. Traditional desalting approaches applied to urine pretreatment suffer from the chemical losses, which reduce the information depth of analysis. We aimed to test a simple approach for the simultaneous preconcentration and desalting of organic solutes in urine based on the collection of induced bursting bubble aerosols above the surface of urine samples. Bursting bubbles were generated at ambient conditions by feeding gas through an air diffuser at the bottom of diluted (200 times in ultrapure water) urine solution (50-500 mL). Collected aerosols were analyzed by the direct-infusion electrospray ionization mass spectrometry (ESI-MS). The simultaneous preconcentration (ca. 6-12 fold) and desalting (ca. 6-10 fold) of organic solutes in urine was achieved by the bursting bubble sample pretreatment, which allowed ca. 3-times higher number of identified urine metabolites by high-resolution MS analysis. No notable chemical discrimination effects were observed. The increased degree of MS data clustering was demonstrated on the principal component analysis of data sets from the urine of healthy people and from the urine people with renal insufficiency. At least 10 times higher sensitivity of trace drug detection in urine was demonstrated for clenbuterol and salbutamol. Our results indicate the high versatility of bubble bursting as a simple pretreatment approach to enhance the chemical depth and sensitivity of urine analysis.
INSTITUTE
Research Center for Obstetrics, Gynecology and Perinatology
DEPARTMENT
Department of System Biology in Reproduction
LABORATORY
Laboratory for Proteomics and Metabolomics of Human Reproduction
Follicular fluid lipidomics reveals lipid alterations by LH addition during IVF cycles
STUDY_SUMMARY
Purpose Ovulation induction protocols are key components for performing assisted reproduction treatments successfully. The objective of the present study was to estimate how LH addition to controlled ovarian stimulation protocols may affect the follicular fluid lipid profile of women undergoing in vitro fertilization treatment. Methods We conducted the study using 28 self-paired samples, 14 per group. The patients received FSH during their first cycle of ovarian stimulation (FSH group). If treatment did not result in pregnancy, the same patients returned for a new cycle and received stimulus with the addition of LH to the previous protocol (Low-dose-LH group). Lipidomics analysis was performed by UPLC-MSE mass spectrometry. Potential lipid biomarkers were identified by the software Progenesis QI. Statistical analysis was performed using the SPSS 18.0 and MetaboAnalyst 2.0 software.
INSTITUTE
Universidade Federal de Sao Paulo
DEPARTMENT
Surgery
LABORATORY
Centro de Pesquisa em Urologia
LAST_NAME
Da Costa
FIRST_NAME
Livia
ADDRESS
Rua Embau 231 - Vila Clementino, Sao Paulo, Sao Paulo, 04039060, Brazil
EMAIL
liviadovale@hotmail.com
PHONE
551138074062
NUM_GROUPS
2
TOTAL_SUBJECTS
28
NUM_FEMALES
14
STUDY_COMMENTS
The groups consists of the same 14 women submitted to two different controlled ovarian stimulation protocols (FSH or LH group)
Heterologous expression and detection of Apratoxins in E. coli
STUDY_TYPE
Organic extraction of E coli cultures harboring apratoxin gene cluster
STUDY_SUMMARY
The apratoxin gene cluster was recovered from fosmid DNA library. The gene set responsible for the biosynthesis of the polyketide backbone was introduced in E. coli BAP strain and expressed at 30C for 24 hours. Two sets of control and experimental samples with culture broth pH adjusted at 8 and 12 respectively was extracted with ethyl acetate and dried.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Kallifidas
FIRST_NAME
Dimitris
ADDRESS
Medical Sciences Building, Rm P5-26, 1600 SW Archer Rd., FL32610
This targeted metabolomic analysis was performed on plasma samples from 39 normal controls (n=18 men and 21 women) and 45 subjects ((n = 22 men and 23 women) who met diagnostic criteria for ME/CFS by Institute of Medicine, Canadian, and Fukuda criteria.
INSTITUTE
University of California, San Diego
DEPARTMENT
The Mitochondrial and Metabolic Disease Center
LAST_NAME
Naviaux
FIRST_NAME
Robert
ADDRESS
214 Dikinson Street, CTF-C102, San Diego, CA, 92103
EMAIL
maviaux@ucsd.edu
PHONE
619-993-2904
NUM_GROUPS
2 groups for men (control and CFS) and 2 groups for women (control and CFS)
The alpha-1A adrenergic receptor agonist A61603 reduces cardiac polyunsaturated fatty acid-Heart raw data
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
Studies of skeletal muscle disuse either in patients on bed rest or experimentally in animals(immobilization) have demonstrated that decreased protein synthesis is common, with transient parallel increases in protein degradation. Muscle disuse atrophy involves a process of transition from slow to fast myosin fiber types 6 . A shift toward glycolysis, decreased capacity for fat oxidation, and substrate accumulation in atrophied muscles have been reported as has accommodation of the liver with an increased gluconeogenic capacity. Recent studies have modeled skeletal muscle disuse by using cyclic stretch of differentiated myotubes (C2C12), which mimics the loading pattern of mature skeletal muscle, followed by cessation of stretch.We utilized this model to determine the metabolic changes using non-targeted metabolomics analysis of the media. We identified increases in amino acids resulting from protein degradation (largely sarcomere) that occurs with muscle atrophy that are involved in feeding the Kreb’s cycle through anaplerosis. Specifically, we identified increased alanine/proline metabolism (significantly elevated proline, alanine, glutamine, and asparagine) and increased -ketoglutaric acid, the proposed Kreb’s cycle intermediate being fed by the alanine/proline metabolic anaplerotic mechanism. Additionally, several unique pathways not clearly delineated in previous studies of muscle unloading were seen, including: 1) elevated ethanolamine and elevated keto-acids (e.g. 2-ketoleucine and 2-keovaline) represent intermediates in the Ehlrich amino acid degradation pathway, which feeds into a metabolic pathway supplying acetyl-CoA and 2-hydroxybutyrate (also significantly increased); and 2) elevated guanine, an intermediate of purine metabolism, was seen at 12 hours unloading. Given the interest in targeting different aspects of the ubiquitin proteasome system to inhibit protein degradation, this C2C12 system may allow the identification of direct and indirect alterations in metabolism due to anaplerosis or through other yet to be identified mechanisms using a non-targeted metabolomics approach.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister Heart Institute
LABORATORY
Mutliple Centers
LAST_NAME
Ilaiwy, WIllis
FIRST_NAME
Amro, Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
The alpha-1A adrenergic receptor agonist A61603 reduces cardiac polyunsaturated fatty acid-Serum raw data
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
Studies of skeletal muscle disuse either in patients on bed rest or experimentally in animals(immobilization) have demonstrated that decreased protein synthesis is common, with transient parallel increases in protein degradation. Muscle disuse atrophy involves a process of transition from slow to fast myosin fiber types 6 . A shift toward glycolysis, decreased capacity for fat oxidation, and substrate accumulation in atrophied muscles have been reported as has accommodation of the liver with an increased gluconeogenic capacity. Recent studies have modeled skeletal muscle disuse by using cyclic stretch of differentiated myotubes (C2C12), which mimics the loading pattern of mature skeletal muscle, followed by cessation of stretch.We utilized this model to determine the metabolic changes using non-targeted metabolomics analysis of the media. We identified increases in amino acids resulting from protein degradation (largely sarcomere) that occurs with muscle atrophy that are involved in feeding the Kreb’s cycle through anaplerosis. Specifically, we identified increased alanine/proline metabolism (significantly elevated proline, alanine, glutamine, and asparagine) and increased -ketoglutaric acid, the proposed Kreb’s cycle intermediate being fed by the alanine/proline metabolic anaplerotic mechanism. Additionally, several unique pathways not clearly delineated in previous studies of muscle unloading were seen, including: 1) elevated ethanolamine and elevated keto-acids (e.g. 2-ketoleucine and 2-keovaline) represent intermediates in the Ehlrich amino acid degradation pathway, which feeds into a metabolic pathway supplying acetyl-CoA and 2-hydroxybutyrate (also significantly increased); and 2) elevated guanine, an intermediate of purine metabolism, was seen at 12 hours unloading. Given the interest in targeting different aspects of the ubiquitin proteasome system to inhibit protein degradation, this C2C12 system may allow the identification of direct and indirect alterations in metabolism due to anaplerosis or through other yet to be identified mechanisms using a non-targeted metabolomics approach.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister Heart Institute
LABORATORY
Mutliple Centers
LAST_NAME
Ilaiwy, WIllis
FIRST_NAME
Amro, Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Metabolic Adaptation of Staphylococcus aureus to Host Immunity
STUDY_TYPE
Metabolomics Analysis of Methicillin-Resistant Staphylococcus aureus (MRSA) to host immunity.
STUDY_SUMMARY
This project is intended to study the metabolic adaptation of Methicillin-Resistant Staphylococcus aureus (MRSA) to host immunity. Because of the nature of the samples RTI RCMRC worked with Dr. Anthony R. Richardson so that the samples would be extracted at the University of North Carolina at Chapel Hill under the condition that were optimized by RTI RCMRC for broad spectrum metabolomics analysis.
Metabolomic changes during active immunization with anti-METH vaccines.
STUDY_SUMMARY
A targeted metabolomics analysis was performed on serum samples from rats immunized with a methamphetamine-like hapten covalently bound to keyhole limpet hemocyanin (KLH) monomers, and controls. The subjects were approximately 300 g adult male Sprague Dawley rats. RTI International RCMRC received pre-immune serum from RI 11-03A (n=12) which is a matched control serum that was collected before starting immunizations, and week 17 bleeds from RI 11-03A (n=12), RI 11-03B (n=8), and RI 11-03C (n=12). The A-C nomenclature denotes A) complete antigen with adjuvant, B) complete antigen without adjuvant and C) only KLH carrier protein and adjuvant without a METH-like hapten. The rats’ serum samples were extracted and prepared for a combined flow injection (FIA) and LC-MS/MS assay (Biocrates AbsoluteIDQ® p180 kit). The Biocrates AbsoluteIDQ® p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) can quantitatively measure ~188 biologically relevant metabolites from five analyte groups (acylcarnitines, amino acids, biogenic amines, glycerophospho- and sphingolipids, and hexoses) on a triple quadrupole mass spectrometer.
Metabolomics of Mice Cohousing and Microbiota Transfer
STUDY_SUMMARY
The mice serum samples were extracted and prepared for a combined flow injection (FIA) and LC-MS/MS assay (Biocrates AbsoluteIDQ® p180 kit). The Biocrates AbsoluteIDQ® p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) can quantitatively measure ~188 biologically relevant metabolites from five analyte groups (acylcarnitines, amino acids, biogenic amines, glycerophospho- and sphingolipids, and hexoses) on a triple quadrupole mass spectrometer.
Cells are treated with vehicle or Doxycycline - to induce expression of GFP or ATG7
STUDY_SUMMARY
AGY571 cells engineered to express Dox-inducible GFP or ATG7 were treated with 500 ng/mL or 1 ug/mL Doxycycline for 48 hours. Assessing the effects of ATG7 reexpression in B cell lymphoma.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
John Cleveland
LAST_NAME
Fernandez
FIRST_NAME
Mario
ADDRESS
12902 Magnolia Drive, MRC 4-West
EMAIL
mario.fernandez@moffitt.org
PHONE
813-745-5140
NUM_GROUPS
5
TOTAL_SUBJECTS
15
STUDY_COMMENTS
Groups collected in triplicate per time point, either treated or untreated with Doxycycline.
Uniquely Tumor-Selective Englerin A Profoundly Alters Lipid Metabolism in Renal Cell Carcinoma inducing ER-Stress and an Acute Inflammatory Response
STUDY_TYPE
Metabolomic effect of Englerin A on renal cell carcinoma
STUDY_SUMMARY
This targeted metabolomic analysis was performed on renal cell carcinoma A498 cells with or without anti-cancer drug Englerin treatment for 24 and 48 h.
INSTITUTE
University of California, San Diego
DEPARTMENT
Department of Pediatrics
LAST_NAME
Batova
FIRST_NAME
Ayse
ADDRESS
La Jolla, CA 92093
EMAIL
abatova@ucsd.edu
PHONE
619-543-1962
NUM_GROUPS
Two groups for 24 h treatment (control and Eglerin treatment) and two groups for 48 h treatment. Each has 4 replicates
Streptococcus mutans organic acids/amino acid profiles, effect of oxidative stress; pilot
STUDY_TYPE
Amino acid/organic acid profiles of wild-type and mutant strain in response to H2O2 treatment over time.
STUDY_SUMMARY
S. mutans UA159 and ΔspxA1 will be grown in BHI to OD600 = 0.4. Each culture will be split in to 4 samples. For the first sample, 3E10 cells will immediately be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. The remaining three samples will be treated with H2O2 to 0.5 mM, and the harvesting process repeated after 15, 30 and 60 minutes.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
Lemos-Abranches
LAST_NAME
Hardin
FIRST_NAME
Emily
ADDRESS
1395 Center Drive, PO Box 100424, Gainesville, FL 32610
Metabolomics of Saliva Samples Obtained from Subjects with Diabetes
STUDY_SUMMARY
In this research, were are investigating the metabolic profile changes associated with well- and poorly-controlled type 1 and 2 diabetes and if there are distinct metabolite compounds that may be associated with glycemic control. The PI of the study collected whole unstimulated saliva samples were from subjects with well- and poorly-controlled type 1 and type 2 diabetes. Subjects were selected based on the level of A1C (<7= well-controlled and >7 = poorly controlled). Saliva samples were shipped to RTI RCMRC for a broad spectrum reverse phase metabolomics analysis.
Enterococcus faecalis nucleotide profiles following mupirocin or decoyinine
STUDY_TYPE
Exposure to mupirocin or decoyinine
STUDY_SUMMARY
Triplicate samples of E. faecalis OG1RF will be grown in FMC-AUG to OD600 = 0.25. The cultures will be split and exposed to DMSO, mupirocin (0.01mg/mL) or decoyinine (0.1mg/mL) for 15 minutes. 6E9 cells will be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation, and stored at -80C until shipment.
INSTITUTE
Univeristy of Florida
DEPARTMENT
SECIM
LABORATORY
Lemos-Abranches
LAST_NAME
Kajfasz
FIRST_NAME
Jessica
ADDRESS
1395 Center Drive, PO Box 100424 Gainesville, FL 32610
Comparison between wild-type and mutant strain, as well as providing varying cell count input for WT
STUDY_SUMMARY
E. faecalis OG1RF and rel/relQ will be grown in FMC-AUG to OD600 = 0.25. 3E10 cells will be harvested by fast filtration, scraped off of membrane into ice-cold PBS, and pelleted by centrifugation. This process will be repeated with OG1RF only to harvest 3E9 and 3E8 cells. A second OG1RF sample of 3E10 cells will be scraped into formic acid; only acid-soluble extract willl be sent for this sample.
INSTITUTE
Univeristy of Florida
DEPARTMENT
SECIM
LABORATORY
Lemos-Abranches
LAST_NAME
Kajfasz
FIRST_NAME
Jessica
ADDRESS
1395 Center Drive, PO Box 100424 Gainesville, FL 32610
Exahustive degradation of nucleotide triphosphates
STUDY_TYPE
Comparison of degradation kinetics
STUDY_SUMMARY
The degradation kinetics of nucleotide triphosphates (ATP, GTP, UTP and CTP) were evaluated under boiling ethanol extraction conditions (95°C) during 0 to 300 minutes.
INSTITUTE
University of Groningen
DEPARTMENT
Analytical Biochemistry
LAST_NAME
Bischoff
FIRST_NAME
Rainer
ADDRESS
Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands
Effect of a complex matrix on the degradation of nucleotide triphosphates
STUDY_TYPE
Comparison of degradation kinetics
STUDY_SUMMARY
The effect of a complex cellular matrix extracted from yeast (S. cerevisiae, strain YSBN6 (MATa; genotype: FY3 ho::HphMX4 derived from the S288C parental strain)) on the degradation profiles of nucleotide triphosphates extracted under typical boiling ethanol conditions was evaluated.
INSTITUTE
University of Groningen
DEPARTMENT
Analytical Biochemistry
LAST_NAME
Bischoff
FIRST_NAME
Rainer
ADDRESS
Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands
Effect of the culture medium on the degradation of nucleotide triphosphates
STUDY_TYPE
Endpoint measurement
STUDY_SUMMARY
The effect of the Verduyn culture medium on the degradation profiles of nucleotide triphosphates extracted under typical boiling ethanol conditions was evaluated.
INSTITUTE
University of Groningen
DEPARTMENT
Analytical Biochemistry
LAST_NAME
Bischoff
FIRST_NAME
Rainer
ADDRESS
Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands
Effect of the chemical environment on the degradation of nucleotide triphosphates
STUDY_TYPE
Endpoint measurement
STUDY_SUMMARY
The influence of particular groups of compounds/metabolites, mainly comprising major central carbon metabolites including amino acids, organic acids, sugar phosphates, coenzymes, etc, on the degradation profiles of nucleotide triphosphates extracted under typical boiling ethanol conditions was evaluated.
INSTITUTE
University of Groningen
DEPARTMENT
Analytical Biochemistry
LAST_NAME
Bischoff
FIRST_NAME
Rainer
ADDRESS
Antonius Deusinglaan 1 (XB20), Building 3226, room 601, 9713 AV Groningen, The Netherlands
Amino Acid Quantifcation of obese patients on a 16 week caloric restriction from Plasma
STUDY_TYPE
timecourse, quantitative measurements of amino acid
STUDY_SUMMARY
Caloric restriction (CR) improves insulin sensitivity and reduces the incidence of diabetes in obese individuals. The underlying mechanisms whereby CR improves insulin sensitivity are not clear. We evaluated the effect of 16 weeks of CR on whole-body insulin sensitivity by pancreatic clamp before and after CR in 11 obese participants (BMI = 35 kg/m2) compared with 9 matched control subjects (BMI = 34 kg/m2). Compared with the control subjects, CR increased the glucose infusion rate needed to maintain euglycemia during hyperinsulinemia, indicating enhancement of peripheral insulin sensitivity. This improvement in insulin sensitivity was not accompanied by changes in skeletal muscle mitochondrial oxidative capacity or oxidant emissions, nor were there changes in skeletal muscle ceramide, diacylglycerol, or amino acid metabolite levels. However, CR lowered insulin-stimulated thioredoxin-interacting protein (TXNIP) levels and enhanced nonoxidative glucose disposal. These results support a role for TXNIP in mediating the improvement in peripheral insulin sensitivity after CR.
Amino Acid Quantifcation of obese patients on a 16 week caloric restriction from muscle biopsy (part II)
STUDY_TYPE
timecourse, quantitative measurements of amino acid
STUDY_SUMMARY
Caloric restriction (CR) improves insulin sensitivity and reduces the incidence of diabetes in obese individuals. The underlying mechanisms whereby CR improves insulin sensitivity are not clear. We evaluated the effect of 16 weeks of CR on whole-body insulin sensitivity by pancreatic clamp before and after CR in 11 obese participants (BMI = 35 kg/m2) compared with 9 matched control subjects (BMI = 34 kg/m2). Compared with the control subjects, CR increased the glucose infusion rate needed to maintain euglycemia during hyperinsulinemia, indicating enhancement of peripheral insulin sensitivity. This improvement in insulin sensitivity was not accompanied by changes in skeletal muscle mitochondrial oxidative capacity or oxidant emissions, nor were there changes in skeletal muscle ceramide, diacylglycerol, or amino acid metabolite levels. However, CR lowered insulin-stimulated thioredoxin-interacting protein (TXNIP) levels and enhanced nonoxidative glucose disposal. These results support a role for TXNIP in mediating the improvement in peripheral insulin sensitivity after CR.
D2 Glucose Quantifcation of obese patients on a 16 week caloric restriction from plasma
STUDY_TYPE
timecourse
STUDY_SUMMARY
Caloric restriction (CR) improves insulin sensitivity and reduces the incidence of diabetes in obese individuals. The underlying mechanisms whereby CR improves insulin sensitivity are not clear. We evaluated the effect of 16 weeks of CR on whole-body insulin sensitivity by pancreatic clamp before and after CR in 11 obese participants (BMI = 35 kg/m2) compared with 9 matched control subjects (BMI = 34 kg/m2). Compared with the control subjects, CR increased the glucose infusion rate needed to maintain euglycemia during hyperinsulinemia, indicating enhancement of peripheral insulin sensitivity. This improvement in insulin sensitivity was not accompanied by changes in skeletal muscle mitochondrial oxidative capacity or oxidant emissions, nor were there changes in skeletal muscle ceramide, diacylglycerol, or amino acid metabolite levels. However, CR lowered insulin-stimulated thioredoxin-interacting protein (TXNIP) levels and enhanced nonoxidative glucose disposal. These results support a role for TXNIP in mediating the improvement in peripheral insulin sensitivity after CR.
Metabolomic profiles along the gastrointestinal tract of the healthy dog
STUDY_SUMMARY
Introduction: The fecal microbiome is relevant to the health and disease of many species. The importance of the fecal metabolome has more recently been appreciated, but our knowledge of the microbiome and metabolome at other sites along the gastrointestinal tract remains deficient. Objective: To analyze the gastrointestinal microbiome and metabolome of healthy domestic dogs at four anatomical sites. Methods: Samples of the duodenal, ileal, colonic, and rectal contents were collected from six adult dogs after humane euthanasia for an unrelated study. The microbiota were characterized using Illumina sequencing of 16S rRNA genes. The metabolome was characterized by mass spectrometry-based methods. Results: Prevalent phyla throughout the samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes, consistent with previous findings in dogs and other species. A total of 530 unique metabolites were detected; 199 of these were identified as previously named compounds, but 141 of them had at least one significantly different site-pair comparison. Noteworthy examples include amino acids, which decreased from the small to large intestine; pyruvate, which was at peak concentrations in the ileum; and several phenol-containing carboxylic acid compounds that increased in the large intestine. Conclusion: The microbiome and metabolome vary significantly at different sites along the canine gastrointestinal tract.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status
STUDY_SUMMARY
Onset of chronic periodontitis is associated with an aberrant polymicrobial community, termed dysbiosis. Findings of a recent model of its etiology suggested that dysbiosis holds a conserved metabolic signature as an emergent property. The purpose of this study was to identify robust biomarkers for periodontal inflammation severity. Furthermore, we investigated disease-associated metabolic signatures of periodontal microbiota using a salivary metabolomics approach. Collection of whole saliva samples was performed before and after removal of supragingival plaque (debridement). Periodontal inflamed surface area (PISA) was employed as an indicator of periodontal inflammatory status. Based on multivariate analyses using pre-debridement salivary metabolomics data, we found that the metabolites associated with higher PISA included cadaverine and hydrocinnamate, while uric acid and ethanolamine were associated with lower PISA. Next, we focused on dental plaque metabolic byproducts by selecting significantly decreased salivary metabolites following debridement. Metabolite set enrichment analysis revealed that polyamine metabolism, arginine and proline metabolism, butyric acid metabolism, and lysine degradation were distinctive metabolic signatures of dental plaque in the high PISA group, which may have relevance to the metabolic signatures of disease-associated communities. Collectively, our findings identified potential biomarkers of periodontal inflammatory status, while they also provide insight into metabolic signatures of dysbiotic communities.
M-CMV-infected N. tabacum plants with six symptoms (vein clearing, mosaic, chlorosis, partial green recovery, complete green recovery and secondary mosaic) were analyzed by LC-MS & GC-MS. In addition, the pathogenesis biomarker might be found by this untargeted global metabolomic analysis.
The goal of this project is to analyze the metabolic pool distribution of cerebral metabolites in response to cocaine administration and withdrawal as compared to control
In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabotype. Additional samples reflecting different stages of date fruit ripening process has been included for 10 different fruit varieties.
Metabolic changes to maternal rat liver tissue during and post-pregnancy
STUDY_SUMMARY
Assessing metabolic changes to maternal rat liver tissue during and post-pregnancy. Liver tissue was harvested post-mortem from rats or mice without pregnancy (Nulliparous - NP), time course during pregnancy in days (P2-4, P11-13m P18-20), lactation day 10 (LD10), in during involution of the liver (I2, I4, I6, I8, I10) and 4-weeks regression after preganancy (R4).
Assessing metabolic changes to maternal rat liver tissue during and post-pregnancy (part II)
STUDY_SUMMARY
Assessing metabolic changes to maternal rat liver tissue during and post-pregnancy. Liver tissue was harvested post-mortem from rats or mice without pregnancy (Nulliparous - NP), time course during pregnancy in days (P2-4, P11-13m P18-20), lactation day 10 (LD10), in during involution of the liver (I2, I4, I6, I8, I10) and 4-weeks regression after preganancy (R4).
Determine how inhibition of autophagy/proteasome degradation or inhibition of protein synthesis in models of muscle insulin resistance affect amino acid metabolites
STUDY_SUMMARY
To determine which protein degradation pathways downstream of IR and IGF1R contribute to changes in amino acid and mitochondrial metabolite pools, we will treat control, M-IR-/-, MIGIRKO, and HFD obese mice with inhibitors of autophagy or proteasome. We will treat 5 animals each of control, M-IR-/-, MIGIRKO, and HFD mice with vehicle, colchicine to inhibit autophagy, or MG132 to inhibit proteasome activity, then measure amino acid in muscle tissue.
Investigating TCA concentrations in mice muscle tissue lacking insulin receptors and IGF-1 receptors
STUDY_SUMMARY
Quantitative measures of TCA cycle metabolites from control, M-IR-/-, M-IGF1R-/- , and MIGIRKO mice. Also compare mice on a chow diet to mice on a high fat diet (HFD).
Inhibition of autophagy/proteasome degradation or inhibition of protein synthesis in models of muscle insulin resistance affect TCA cycle
STUDY_SUMMARY
To determine which protein degradation pathways downstream of IR and IGF1R contribute to changes in amino acid and mitochondrial metabolite pools, we will treat control, M-IR-/-, MIGIRKO, and HFD obese mice with inhibitors of autophagy or proteasome. We will treat 5 animals each of control, M-IR-/-, MIGIRKO, and HFD mice with vehicle, colchicine to inhibit autophagy, or MG132 to inhibit proteasome activity, then measure TCA cycle in muscle tissue.
Inhibition of autophagy/proteasome degradation or inhibition of protein synthesis in models of muscle insulin resistance affect amino acids metabolites in serum
STUDY_SUMMARY
To determine which protein degradation pathways downstream of IR and IGF1R contribute to changes in amino acid and mitochondrial metabolite pools, we will treat control, M-IR-/-, MIGIRKO, and HFD obese mice with inhibitors of autophagy or proteasome. We will treat 5 animals each of control, M-IR-/-, MIGIRKO, and HFD mice with vehicle, colchicine to inhibit autophagy, or MG132 to inhibit proteasome activity, then measure amino acid metabolites in serum.
Metabolomics of longitudinal plasma samples from Macaca mulatta infected with Plasmodium cynomolgi B strain.
STUDY_TYPE
Longitudinal parasite infection and treatment of multiple individuals
STUDY_SUMMARY
Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for parasitological, clinical, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug Artemether was subcuratively administered selectively to several subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications. The anti-malarial drugs Primaquine and Chloroquine were administered to all remaining subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Plasma samples were acquired every other day from capillary blood and during seven-time point collections of venous blood. Supplemental files, including a ReadMe with additional experimental details, all raw data, and analytical metadata, are provided as part of this submission.
INSTITUTE
Emory University
DEPARTMENT
School of Medicine, Vaccine Center at Yerkes
LAST_NAME
Karpuzoglu
FIRST_NAME
Ebru
ADDRESS
Emory University, 954 Gatewood Rd, Room 208, Atlanta, GA 30329
EMAIL
mahpic@emory.edu
PHONE
N/A
TOTAL_SUBJECTS
5
STUDY_COMMENTS
Malaria Host Pathogen Interaction Center Experiment 04, 5 subjects 286 samples, "The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 04' (E04). To access other publicly available results from E04 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public."
Measuring amino acid metabolites in insulin resistant and insulin deficient mouse tissue models
STUDY_SUMMARY
To compare models of insulin resistance to a model of loss of insulin signaling, we will also determine amino acid metabolites from muscle, using control and streptozotocin (STZ) treated mice as a model of insulin deficient diabetes.
Measuring acylcarnitine concentrations in insulin resistant and insulin deficient mouse tissue models
STUDY_SUMMARY
To compare models of insulin resistance to a model of loss of insulin signaling, we will also determine muscle acylcarnitine concentrations, using control and streptozotocin (STZ) treated mice as a model of insulin deficient diabetes. Changes in metabolite profiles will be correlated with activation of mTOR and FoxO pathways in muscle.
Measuring ceramide concentrations in insulin resistant and insulin deficient mouse tissue models
STUDY_SUMMARY
To compare models of insulin resistance to a model of loss of insulin signaling, we will also determine ceramide concentration in muscle, using control and streptozotocin (STZ) treated mice as a model of insulin deficient diabetes.
Investigating ceremide concentrations in mice muscle tissue lacking insulin receptors and IGF-1 receptors
STUDY_SUMMARY
Quantitative measures of ceramide metabolite concentrations in muscle from control, M-IR-/-, M-IGF1R-/- , and MIGIRKO mice. Also compare mice on a chow diet to mice on a high fat diet (HFD).
Measuring TCA cycle concentrations in insulin resistant and insulin deficient mouse tissue models
STUDY_SUMMARY
To compare models of insulin resistance to a model of loss of insulin signaling, we will also determine TCA cycle metabolites in muscle, using control and streptozotocin (STZ) treated mice as a model of insulin deficient diabetes.
Measuring NEFA concentrations in insulin resistant and insulin deficient mouse tissue models
STUDY_SUMMARY
To compare models of insulin resistance to a model of loss of insulin signaling, we will also determine nonesterified fatty acid metabolites in muscle, using control and streptozotocin (STZ) treated mice as a model of insulin deficient diabetes.
Plasma metabolomics profiling for fish maturation in blunt snout bream
STUDY_TYPE
Metabolomics experiment
STUDY_SUMMARY
We investigated the comprehensive metabolic profiles of plasma among immature females, mature females ready to spawn, as well as already spawned breeders of blunt snout bream (Megalobrama amblycephala). The purpose of this study was to screen out potential biomarkers for sexual mature female M. amblycephala compared to immature female individuals and already spawned breeders. The three groups were set up in this study, including one year old immature females, 2 years old sexually mature females ready to spawning and successfully spawning females of M. amblycephala. The plasma samples were collected to investigate the comprehensive metabolic profiles through UPLC-MS/MS based metabolomics analysis method. According to multivariate and univariate statistical analysis, plasma metabolite profiles of three groups were obviously separated, and the plasma metabolite profiles of immature female M. amblycephala were much more different from mature females ready to spawn as well as already spawned breeders. The differential plasma metabolites from three hormone related pathways including GnRH signaling pathway, steroid hormone biosynthesis and steroid biosynthesis, were further analyzed. A total of 29 metabolites were identified as differential biomarkers associated with the female maturation status
INSTITUTE
Huazhong Agricultural University, Wuhan
DEPARTMENT
College of Fisheries
LABORATORY
Key Lab of Freshwater Animal Breeding, Ministry of Agriculture
Effects of Curcumin Supplementation on the Amino Acid Concentration of Older Adults: Relation to Vascular Function
STUDY_SUMMARY
Perform amino acid concentrations metabolite analysis related to nitric oxide biology, oxidative stress and inflammation in plasma before and after 12 weeks of oral curcumin (2000 mg/d) or placebo (double-blind, randomized) in men and women aged 45-79 years who are free from clinical cardiovascular disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Seals
FIRST_NAME
Douglas
ADDRESS
Department of Integrative Physiology University of Colorado Boulder, CO 80309
Effects of Curcumin Supplementation on the Non‐Esterified Fatty Acids concentration of Older Adults: Relation to Vascular Function
STUDY_SUMMARY
Perform non-esterified fatty acid concentrations metabolite analysis related to nitric oxide biology, oxidative stress and inflammation in plasma before and after 12 weeks of oral curcumin (2000 mg/d) or placebo (double-blind, randomized) in men and women aged 45-79 years who are free from clinical cardiovascular disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Seals
FIRST_NAME
Douglas
ADDRESS
Department of Integrative Physiology University of Colorado Boulder, CO 80309
Effects of Curcumin Supplementation on the Ceramides Concentration of Older Adults: Relation to Vascular Function
STUDY_SUMMARY
Perform ceramides concentrations metabolite analysis related to nitric oxide biology, oxidative stress and inflammation in plasma before and after 12 weeks of oral curcumin (2000 mg/d) or placebo (double-blind, randomized) in men and women aged 45-79 years who are free from clinical cardiovascular disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Seals
FIRST_NAME
Douglas
ADDRESS
Department of Integrative Physiology University of Colorado Boulder, CO 80309
Effects of Curcumin Supplementation on the Acylcarnitine Concentration of Older Adults: Relation to Vascular Function
STUDY_SUMMARY
Perform acylcarnitine concentrations metabolite analysis related to nitric oxide biology, oxidative stress and inflammation in plasma before and after 12 weeks of oral curcumin (2000 mg/d) or placebo (double-blind, randomized) in men and women aged 45-79 years who are free from clinical cardiovascular disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Seals
FIRST_NAME
Douglas
ADDRESS
Department of Integrative Physiology University of Colorado Boulder, CO 80309
Our aim is to identify the LSR-driven metabolomics profile of breast cancer cells in lean and obesogenic environments. Breast cancer cell models with high or undetectable levels of LSR, including drug resistance models, were cultured in lean and obesogenic environments and comprehensive metabolomics profiling, including lipidomics-focused sub-analyses were performed. The metabolomics analyses using both approaches will help us determine if LSR enhances aggressive breast cancer phenotypes via modulation of cellular bioenergetic metabolism, ultimately contributing to poor patient outcome.
Broad spectrum, reverse phase LCMS metabolomics (Negative ion mode)
STUDY_SUMMARY
Our aim is to identify the LSR-driven metabolomics profile of breast cancer cells in lean and obesogenic environments. Breast cancer cell models with high or undetectable levels of LSR, including drug resistance models, were cultured in lean and obesogenic environments and comprehensive metabolomics profiling, including lipidomics-focused sub-analyses were performed. The metabolomics analyses using both approaches will help us determine if LSR enhances aggressive breast cancer phenotypes via modulation of cellular bioenergetic metabolism, ultimately contributing to poor patient outcome.
Effects of herb DG and KK01 on Type 2 Diabetes Mellitus (T2DM) through Lipidomics
STUDY_TYPE
LC-MS lipidomics
STUDY_SUMMARY
According to the results in animal test, KK01 is effective in controlling blood glucose increase with comparable effect as metformin and rosiglitazone. This study will conduct lipid profile comparison for serum samples generated from the animal tests. The comparison will be based on the following groups: 1) db/db mice + DG-high dose; 2) db/db mice +DG-low dose; 3) db/db mice + KK01-high dose; 4) db/db mice + KK01-low dose; 5) db/db mice + metformin; 6) db/db mice + rosiglitazone; 7) db/db mice + saline (disease model); and 8) wild type mice + saline (healthy model). The determined lipid marker(s) will be applied to elucidate the drug target(s) and mechanisms of DG and KK01. Furthermore, comparison of target(s) between KK01 and the first line drugs in diabetic treatment, e.g., metformin and rosiglitazone, will facilitate the finding of featured pathway(s) of KK01 differentiated from the established drugs. Comparison of drug target(s) between KK01 and DG can help to understand the synergistic effects of multiple constituents in the herb.
Kidney tissue metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
This metabolomics study evaluated kidney tissue from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.
INSTITUTE
RTI International
DEPARTMENT
Discovery-Sciences-Technology (DST)
LABORATORY
NIH Eastern Regional Comphrehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E Cornwallis Road, Research Triangle Park, NC 27709
Canine Diabetes - Preliminary Evaluation of Testing Methods
STUDY_TYPE
Single time point blood collection
STUDY_SUMMARY
Blood was collected from diabetic dogs and healthy control dogs. Diabetic dogs and control dogs were breed matched where possible. Timing of blood collection after a meal was matched as best as possible. Serum was frozen at -80C.
Triple Quadrupole Mass Spectrometer to measure low abundance isotope enrichment in individual muscle proteins
STUDY_TYPE
isotope encrichment and comparison of mass spectrometer platforms, timecourse
STUDY_SUMMARY
Stable isotope-labeled amino acids have long been used to measure the fractional synthesis rate of proteins, although the mass spectrometry platforms used for such analyses have changed throughout the years. More recently, tandem mass spectrometers such as triple quadrupoles have been accepted as the standard platform for enrichment measurement due to their sensitivity and the enhanced specificity offered by multiple reaction monitoring (MRM) experiments. The limit in the utility of such platforms for enrichment analysis occurs when measuring very low levels of enrichment from small amounts of sample, particularly proteins isolated from two-dimensional gel electrophoresis (2D-GE), where interference from contaminant ions impact the sensitivity of the measurement. We therefore applied a high resolution orbitrap mass spectrometer to the analysis of [ring-13C6]-phenylalanine enrichment in individual muscle proteins isolated with 2D-GE. Comparison of samples analyzed on both platforms revealed that the high resolution MS has significantly improved sensitivity relative to the triple quadrupole MS at very low-level enrichments due to its ability to resolve interferences in the m/z dimension.
High Resolution orbittrap Mass Spectrometer to measure low abundance isotope enrichment in individual muscle proteins
STUDY_TYPE
isotope encrichment and comparison of mass spectrometer platforms
STUDY_SUMMARY
Stable isotope-labeled amino acids have long been used to measure the fractional synthesis rate of proteins, although the mass spectrometry platforms used for such analyses have changed throughout the years. More recently, tandem mass spectrometers such as triple quadrupoles have been accepted as the standard platform for enrichment measurement due to their sensitivity and the enhanced specificity offered by multiple reaction monitoring (MRM) experiments. The limit in the utility of such platforms for enrichment analysis occurs when measuring very low levels of enrichment from small amounts of sample, particularly proteins isolated from two-dimensional gel electrophoresis (2D-GE), where interference from contaminant ions impact the sensitivity of the measurement. We therefore applied a high resolution orbitrap mass spectrometer to the analysis of [ring-13C6]-phenylalanine enrichment in individual muscle proteins isolated with 2D-GE. Comparison of samples analyzed on both platforms revealed that the high resolution MS has significantly improved sensitivity relative to the triple quadrupole MS at very low-level enrichments due to its ability to resolve interferences in the m/z dimension.
Multi-omics based identification of specific biochemical changes associated with PfKelch13-mutant artemisinin resistant Plasmodium
STUDY_TYPE
Cell type comparison
STUDY_SUMMARY
Two clonaly artemisinin resistant parasitised red blood cells (trophozoite stage) were compared with artemsinin sensitive parasitised red blood cells by metabolomics analysis.
INSTITUTE
Monash Institute of Pharmaceutical Sciences, Monash University
DEPARTMENT
Drug Delivery, Disposition and Dynamics
LABORATORY
Creek lab
LAST_NAME
Creek
FIRST_NAME
Darren
ADDRESS
381 Royal Parade, Parkville, Melbourne, VIC3052, Australia
Inbred mice are used to investigate many aspects of human physiology, including susceptibility to disease and response to therapies. Despite increasing evidence that the composition and function of the murine intestinal microbiota can substantially influence a broad range of experimental outcomes, relatively little is known about microbiome dynamics within experimental mouse populations. We investigated changes in the intestinal microbiome between C57BL/6J mice spanning six generations (assessed at generations 1, 2, 3 and 6), following their introduction to a stringently controlled facility. Faecal microbiota composition and function were assessed by 16S rRNA gene amplicon sequencing and liquid chromatography mass spectrometry, respectively. Significant divergence of the intestinal microbiota between founder and second generation mice, as well as continuing inter-generational variance, was observed. Bacterial taxa whose relative abundance changed significantly included Akkermansia, Turicibacter and Bifidobacterium (p< 0.05), all of which are recognised as having the potential to substantially influence host physiology. Shifts in microbiota composition were mirrored by corresponding differences in the faecal metabolome (r=0.57, p=0.0001), with notable differences in levels of tryptophan pathway metabolites and amino acids, including glutamine, glutamate and aspartate. The magnitude of these changes in the intestinal microbiota and metabolome characteristics during acclimation were on a scale with those observed between populations housed in separate facilities, which differed in regards to husbandry, barrier conditions and dietary intake. The microbiome variance reported here has major implications for experimental reproducibility, and as a consequence, experimental design and the interpretation of research outcomes across as wide range of contexts.
INSTITUTE
South Australian Health and Medical Research Institute
DEPARTMENT
Infection and Immunity Theme
LAST_NAME
Rogers
FIRST_NAME
Geraint
ADDRESS
SAHMRI, North Terrace, Adelaide, SA 5000, Australia
Replication study: The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate
STUDY_SUMMARY
The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered Report describes the proposed replication plan of key experiments from “The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate” by Ward and colleagues, published in Cancer Cell in 2010 (Ward et al., 2010). The experiments that will be replicated are those reported in Figures 2, 3 and 5. Ward and colleagues demonstrate the mutations in isocitrate dehydrogenase 2 (IDH2), commonly found in acute myeloid leukemia (AML), abrogate the enzyme’s wild-type activity and confer to the mutant neomorphic activity that produces the oncometabolite 2-hydroxyglutarate (2-HG) (Figures 2 and 3). They then show that elevated levels of 2-HG are correlated with mutations in IDH1 and IDH2in AML patient samples (Figure 5). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange and the results of the replications will be published by eLife.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
Investigating large scale metabolomics in mice serum lacking insulin receptors and IGF-1 receptors
STUDY_SUMMARY
Large scale metabolomics from control, M-IR-/-, M-IGF1R-/- , and MIGIRKO mice serum. Also compare mice on a chow diet to mice on a high fat diet (HFD).
Metabolomics marker of brown adipose tissue in men
STUDY_SUMMARY
Objective: We aimed to identify metabolites in serum that are associated with BAT volume and activity in men. Methods: We assessed 163 metabolites in fasted serum of a cohort of twenty two healthy lean men (age 24.1 (21.7 – 26.6) years, BMI 22.1 (20.5 – 23.4) kg/m2) who subsequently underwent a cold-induced [18F]FDG PET-CT scan to assess BAT volume and activity. In addition, we included three replication cohorts consisting of in total thirty-seven healthy lean men that were similar with respect to age and BMI compared to the discovery cohort.
Investigating large scale metabolomics in mice tissue lacking insulin receptors and IGF-1 receptors
STUDY_SUMMARY
Large scale metabolomics from control, M-IR-/-, M-IGF1R-/- , and MIGIRKO mice tissue. Also compare mice on a chow diet to mice on a high fat diet (HFD).
The goal of this project is to analyze the metabolic pool distribution of cerebral metabolites in response to cocaine administration and withdrawal as compared to control
IROA feasibility project; plasticizers as obesogens in zebrafish
STUDY_TYPE
(1) IROA label (2) Zebrafish exposed to DEHP
STUDY_SUMMARY
Zebrafish were fed IROA labelled nematodes (smaple 1-4); In a second experiment, zebrafish larvae were exposed to DEHP, a chemical that is a suspected obesogen.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Martyniuk
FIRST_NAME
Chris
ADDRESS
2187 Mowry Rd. Bldg 471
EMAIL
cmartyn@ufl.edu
PHONE
352-294-4636
NUM_GROUPS
2
TOTAL_SUBJECTS
20
STUDY_COMMENTS
Expt 2: Two groups (control) + DEHP-treated (n=10 larvae pools or biological replicates)
Plasma metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model
STUDY_SUMMARY
This metabolomics study evaluated plasma from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.
INSTITUTE
RTI International
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E. Cornwallis Road, Research Triangle Park, NC 27709
Urine metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.
STUDY_SUMMARY
This metabolomics study evaluated urine from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.
INSTITUTE
RTI International
LABORATORY
NIH Eastern Regional Comphrehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E. Cornwallis Road, Research Triangle Park, NC 27709
Metabolomics of immunoglobulin-producing cells in IgA nephropathy
STUDY_SUMMARY
IgA nephropathy (IgAN), the most common primary glomerulonephritis, is characterized by deposits of IgA-containing immune complexes in the kidney glomeruli, as first described by Berger and Hinglais in 1968. IgAN is a major cause of end-stage renal disease with its associated cardio-renal morbidity and mortality. Analyses of the IgA deposits revealed that the IgA is exclusively of the IgA1 subclass and that this IgA1 is aberrantly glycosylated, deficient in galactose in some O-glycans (Gd-IgA1). Patients with IgAN have elevated serum levels of Gd-IgA1 bound by anti-glycan autoantibodies in circulating immune complexes (CIC) that are fundamental in driving disease pathology in an autoimmune process. We have recently shown that elevated serum levels of Gd-IgA1 in patients with IgAN predict disease progression. Thus, understanding the mechanisms behind Gd-IgA1 production will improve future treatment options, as there is presently no disease-specific therapy. A total of 24 cell pellets (4 replicates from 6 cell lines) were analyzed by LCMS metabolomics. Immortalized immunoglobulin-producing cell lines were generated from peripheral-blood lymphocytes from patients with IgAN and healthy controls as described in Suzuki, H., Moldoveanu, Z., Hall, S., et al. IgA1-secreting cell lines from patients with IgA nephropathy produce aberrantly glycosylated IgA1. J Clin Invest. 2008, 118, 629-639.
INSTITUTE
RTI International
LABORATORY
NIH Eastern Regional Comphrehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E. Cornwallis Road, Research Triangle Park, NC 27709
In this study the F8 population of 100 Recombinant Inbred Lines (RILs) obtained from a cross between Solanum lycopersicum X Solanum pimpinellifolium were intelligently allocated to two sub-populations optimized for the distribution of parental alleles using the R-procedure DesignGG (Li et al., 2009; Joosen et al., 2013); hence 50 RIL lines were used for dry seeds and 50 lines for 6h imbibed seeds
INSTITUTE
Wageningen UR
DEPARTMENT
Plant Physiology
LABORATORY
Wageningen Seed Lab, Lab
LAST_NAME
Ligterink
FIRST_NAME
Wilco
ADDRESS
Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
Maize plants were grown under three different temperature regimes: 1) normal day / normal night; 2) hot day / normal night; 3) hot day / hot night. Kernels from developing ears were taken 14, 16, 18, 22, 26 and 40 days after pollination.
Association of hemodialysis patient plasma trace metals with response to erythropoiesis stimulating agents
STUDY_TYPE
Metallomics
STUDY_SUMMARY
EDTA-Plasma from 110 hemodialysis patients participating in an NIDDK funded study were analyzed by ICP-MS for the concentration of As, Cd, Co, Cr, Cu, Mn, Mo, Ni, Pb, Sb, Se, Sn, V, and Zn. Associations were determined between trace metals and gender, race, hemodialysis status, hemoglobin at the time of draw (Hgb), total ESA dose for the month the sample was collected (EPO), and erythropoietin resistance index determined over the 6 months of treatment leading up to sample collection (ERI)
INSTITUTE
RTI International
LABORATORY
NIH Eastern Regional Comprehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)
LAST_NAME
Sumner
FIRST_NAME
Susan
ADDRESS
3040 E. Cornwallis Road, Research Triangle Park, NC 27709, USA
Large Scale C18 Profiling of the Effects of Curcumin Supplementation of Older Adults: Relation to Vascular Function
STUDY_SUMMARY
Perform large scale profiling C18 metabolite analysis related to nitric oxide biology, oxidative stress and inflammation in plasma before and after 12 weeks of oral curcumin (2000 mg/d) or placebo (double-blind, randomized) in men and women aged 45-79 years who are free from clinical cardiovascular disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Seals
FIRST_NAME
Douglas
ADDRESS
Department of Integrative Physiology University of Colorado Boulder, CO 80309
Large Scale HILIC Profiling of the Effects of Curcumin Supplementation of Older Adults: Relation to Vascular Function
STUDY_SUMMARY
Perform large scale profiling HILIC metabolite analysis related to nitric oxide biology, oxidative stress and inflammation in plasma before and after 12 weeks of oral curcumin (2000 mg/d) or placebo (double-blind, randomized) in men and women aged 45-79 years who are free from clinical cardiovascular disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Seals
FIRST_NAME
Douglas
ADDRESS
Department of Integrative Physiology University of Colorado Boulder, CO 80309
Metabolomic study on a schizophrenia and type 2 diabetes susceptibility gene
STUDY_SUMMARY
a comprehensive serum metabolomic analysis in healthy subjects with different genotypes of rs12742393 (n=49 for AA, AC, and CC, respectively) using gas chromatography–time-of-flight mass spectrometry and ultra-performance liquid chromatography quadruple time-of-flight mass spectrometry.
INSTITUTE
Shanghai Jiao Tong University Affiliated Sixth People’s Hospital
Metabolome analysis of the cecal contents of GF mice and GF mice colonized with dominant gut microbes present in the ceca of neonatal and adult mice
STUDY_SUMMARY
Metabolome profiles of GF or GF mice reconstituted with Esherichia coli (EC), Bacteroides acidifaciens (Bac), or Clostridia consortium (CL) were compared.
Effects of the Kinase Inhibitor Sorafenib on Serum Metabolism In Vivo using Non-targeted Metabolomics Analysis tissue).
STUDY_SUMMARY
The human kinome consists of ~500 kinases, including 150 proposed as therapeutic targets. progression, cell death, differentiation, and survival. It is not surprising, then, that new tyrosine kinase inhibitors (TKIs) developed to treat cancer also exhibit cardiotoxicity, including sorafenib. We hypothesized that sorafenib cardiotoxicity is related to its deleterious effects on specific cardiac metabolic pathways given the critical role of TKs in cardiac metabolism. FVB/N mice (10/group) were challenged with sorafenib or vehicle control daily for two weeks. Echocardiographic assessment of the heart identified systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Cardiac, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Compared to vehicle treated controls, sorafenib-treated hearts exhibited significant alterations in 11 metabolites, including markedly altered taurine/hypotaurine metabolism by pathway enrichment analysis (25-fold enrichment). These studies identify sorafenib-induced alterations in cardiac alanine and taurine/hypotaurine metabolic. Interventions to rescue or prevent sorafenib-related cardiotoxicity warrant consideration of therapies targeting the taurine/hypotaurine deficiency identified in the current study.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Effects of the Kinase Inhibitor Sorafenib on Muscle Metabolism In Vivo using Non-targeted Metabolomics Analysis tissue).
STUDY_SUMMARY
The human kinome consists of ~500 kinases, including 150 proposed as therapeutic targets. progression, cell death, differentiation, and survival. It is not surprising, then, that new tyrosine kinase inhibitors (TKIs) developed to treat cancer also exhibit cardiotoxicity, including sorafenib. We hypothesized that sorafenib cardiotoxicity is related to its deleterious effects on specific cardiac metabolic pathways given the critical role of TKs in cardiac metabolism. FVB/N mice (10/group) were challenged with sorafenib or vehicle control daily for two weeks. Echocardiographic assessment of the heart identified systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Cardiac, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Compared to vehicle treated controls, sorafenib-treated hearts exhibited significant alterations in 11 metabolites, including markedly altered taurine/hypotaurine metabolism by pathway enrichment analysis (25-fold enrichment). These studies identify sorafenib-induced alterations in cardiac alanine and taurine/hypotaurine metabolic. Interventions to rescue or prevent sorafenib-related cardiotoxicity warrant consideration of therapies targeting the taurine/hypotaurine deficiency identified in the current study.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Effects of the Kinase Inhibitor Sorafenib on Heart Metabolism In Vivo using Non-targeted Metabolomics Analysis tissue).
STUDY_SUMMARY
The human kinome consists of ~500 kinases, including 150 proposed as therapeutic targets. progression, cell death, differentiation, and survival. It is not surprising, then, that new tyrosine kinase inhibitors (TKIs) developed to treat cancer also exhibit cardiotoxicity, including sorafenib. We hypothesized that sorafenib cardiotoxicity is related to its deleterious effects on specific cardiac metabolic pathways given the critical role of TKs in cardiac metabolism. FVB/N mice (10/group) were challenged with sorafenib or vehicle control daily for two weeks. Echocardiographic assessment of the heart identified systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Cardiac, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Compared to vehicle treated controls, sorafenib-treated hearts exhibited significant alterations in 11 metabolites, including markedly altered taurine/hypotaurine metabolism by pathway enrichment analysis (25-fold enrichment). These studies identify sorafenib-induced alterations in cardiac alanine and taurine/hypotaurine metabolic. Interventions to rescue or prevent sorafenib-related cardiotoxicity warrant consideration of therapies targeting the taurine/hypotaurine deficiency identified in the current study.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Effects of the Kinase Inhibitor Sorafenib on Liver Metabolism In Vivo using Non-targeted Metabolomics Analysis tissue).
STUDY_SUMMARY
The human kinome consists of ~500 kinases, including 150 proposed as therapeutic targets. progression, cell death, differentiation, and survival. It is not surprising, then, that new tyrosine kinase inhibitors (TKIs) developed to treat cancer also exhibit cardiotoxicity, including sorafenib. We hypothesized that sorafenib cardiotoxicity is related to its deleterious effects on specific cardiac metabolic pathways given the critical role of TKs in cardiac metabolism. FVB/N mice (10/group) were challenged with sorafenib or vehicle control daily for two weeks. Echocardiographic assessment of the heart identified systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Cardiac, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Compared to vehicle treated controls, sorafenib-treated hearts exhibited significant alterations in 11 metabolites, including markedly altered taurine/hypotaurine metabolism by pathway enrichment analysis (25-fold enrichment). These studies identify sorafenib-induced alterations in cardiac alanine and taurine/hypotaurine metabolic. Interventions to rescue or prevent sorafenib-related cardiotoxicity warrant consideration of therapies targeting the taurine/hypotaurine deficiency identified in the current study.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Experiment HuA: Metabolomics of plasma samples from humans infected with Plasmodium vivax strain.
STUDY_TYPE
Longitudinal study and treatment of multiple individuals with Chloroquine
STUDY_SUMMARY
Patients with vivax malaria were enrolled in this study from June 2011 to December 2012 at the Fundacão de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), an infectious disease referral center located in Manaus, Western Brazilian Amazon. This study, which required a 42-day follow-up period, was approved by the FMT-HVD Institutional Review Board and the Brazilian National Ethics Committee (CONEP) (IRB approval #: CAAE: 12516713.8.0000.0005). All protocols and documentation were reviewed and sample shipments approved by the Emory IRB. Male and female patients were eligible for inclusion if aged 6 months to 60 years, bodyweight ?5 kg, presenting a blood parasite density from 250 to 100,000 parasites/microliter and axillary temperature ?37.5°C or history of fever in the last 48 hours. Exclusion criteria were: use of antimalarials in the previous 30 days, refusal to be followed up for 42 days and any clinical complication. Patients received supervised treatment with 25 mg/kg of chloroquine (CQ) phosphate over a 3-day period (10 mg/kg on day 0 and 7.5 mg/kg on days 1 and 2). Primaquine (0.5 mg/kg per day for 7 days) was prescribed at the end of the 42-day follow-up period. Patients who vomited the first dose within 30 minutes after drug ingestion were re-treated with the same dose. Patients were evaluated on days 0, 1, 2, 3, 7, 14, 28 and 42 and, if they felt ill, at any time during the study period. Blood smear readings, complete blood counts, and diagnostic polymerase chain reaction (PCR) amplifications were performed at all time points. Three aliquots of 100 µL of whole blood from the day of a recurrence were spotted onto filter paper for later analysis by high performance liquid chromatography (HPLC) to estimate the levels of CQ and desethylchloroquine (DCQ) as previously described. In this study, CQ-resistance with parasitological failure was defined as parasite recurrence in the presence of plasma concentrations of CQ and DSQ higher than 100 ng/mL and microsatellite analysis revealing the presence of the same clonal nature at diagnosis and recurrence. The CQ-sensitive control group consisted of patients with no parasitemia recurring during follow-up period. A group of 20 healthy individuals from Brazil was used as non-malarial control group. Within the MaHPIC, this project is known as ‘Experiment HuA’. This dataset was produced by Dean Jones at Emory University.
INSTITUTE
Emory University
DEPARTMENT
School of Medicine, Vaccine Center at Yerkes
LAST_NAME
Galinksi
FIRST_NAME
Mary
ADDRESS
Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
AH and TM samples were obtained from young-normotensive DBA/2J (3 and 7.5 months) and old-hypertensive DBA/2J mice (8-8.5, 10 and 12 month). Lipids were extracted using modified Bligh and Dyer method and subjected to mass spectrometric identification using appropriate class-specific lipid standards and ratiometric quantification. Corresponding aqueous phase (of extraction) protein concentrations were measured using Bradford method.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
AH and TM samples were obtained from young-normotensive DBA/2J (3 and 7.5 months) and old-hypertensive DBA/2J mice (8-8.5, 10 and 12 month). Lipids were extracted using modified Bligh and Dyer method and subjected to mass spectrometric identification using appropriate class-specific lipid standards and ratiometric quantification. Corresponding aqueous phase (of extraction) protein concentrations were measured using Bradford method.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
AH and TM samples were obtained from young-normotensive DBA/2J (3 and 7.5 months) and old-hypertensive DBA/2J mice (8-8.5, 10 and 12 month). Lipids were extracted using modified Bligh and Dyer method and subjected to mass spectrometric identification using appropriate class-specific lipid standards and ratiometric quantification. Corresponding aqueous phase (of extraction) protein concentrations were measured using Bradford method.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
AH and TM samples were obtained from young-normotensive DBA/2J (3 and 7.5 months) and old-hypertensive DBA/2J mice (8-8.5, 10 and 12 month). Lipids were extracted using modified Bligh and Dyer method and subjected to mass spectrometric identification using appropriate class-specific lipid standards and ratiometric quantification. Corresponding aqueous phase (of extraction) protein concentrations were measured using Bradford method.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
The Metabolomics of Oral Biofilms exposed to Arginine and Fluoride
STUDY_SUMMARY
The study aims to use global metabolomics to investigate: (1) the metabolic profile of supragingival dental plaque from adults with different caries-status and from specific healthy and carious tooth-sites; and (2) the metabolic changes occurring in response to the use of the arginine or fluoride toothpastes for 12 weeks.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
Nascimento/Garrett
LAST_NAME
Nascimento
FIRST_NAME
Marcelle
ADDRESS
1395 Center Drive, Room D9-6, PO Box 100415, Gainesville, FL 32610-0415
Fasting wildtype, tfeb -/- knockout, and lmna -/- knockout metabolite profiling of adult zebrafish
STUDY_SUMMARY
Inhibition of mechanistic target of rapamycin (mTOR) activity exerts cardioprotective functions. We propose to assess the metabolite profile in zebrafish cardiomyopathy models to test the cardioprotective role of mTOR-TFEB-autophagy and mTOR-lmna- autophagy signaling in heart, liver, muscle, brain, and kidney tissue. In addition mTOR signaling among zebrafish 2 hour post feeding, 24 hour post feeding, and 48 hour post feeding will be profiled. These studes will be used as a baseline and for protocol development before we assess changes in DOX-induced cardiomyopathy.
METABOLOMIC PROFILING OF FOLLICULAR FLUID FROM PATIENTS WITH INFERTILITY-RELATED DEEP ENDOMETRIOSIS.
STUDY_SUMMARY
the metaboloc qualitative profiling was performed by LC-MS in follicular fluid samples of controls and endometriosis patients undergoing in vitro fertilization treatment
Evaluation of specific concentrations for use in experimental protocol
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
This study evaluated specific plasma concentrations and compared the optimal plasma extract volume established in the first study (Effects of dilution on analyte identification and quantification) with the volume previously used in the current institutional protocol. The findings of this study lead to recommendations for experimental design in GC-MS-based metabolomic profiling of human plasma.
Effects of dilution on analyte identification and quantification
STUDY_TYPE
GC-MS non-targeted metabolomic profiling
STUDY_SUMMARY
The limiting-dilution study evaluated the effects of sample dilution on the ability to identify and quantify analytes in plasma. The study was divided into 10 batches with identical experimental design spanning over a 16-day period. Each batch consisted of 33 aliquots with 11 different plasma extract volumes (0 – 700 µL) corresponding to 11 plasma concentrations repeated three times.
Metablomic profiling in acc1-5 mutant and wild type arabidiopsis
STUDY_SUMMARY
This experiment tests the metabolic consequence of a mutation at the ACC1 gene (At1g36160). The allele of acc1-5 bearing an EMS mutation, which cause a single amino acid substitution from aspartic acid to asparagine. Seedlings from both the acc1-5 mutant and the wild type were harvested and analyzed via HILIC LC-MS. Of particular interest are metabolites which would be affected by depletion of malonyl-CoA pools (flavenoids) and primary metabolites.
Experiment 13: Uninfected Macaca mulatta exposed to pyrimethamine to produce and integrate clinical, hematological, and omics control measures.
STUDY_SUMMARY
Uninfected, malaria-naive, male rhesus macaques (Macaca mulatta), approximately two years of age, were inoculated intravenously with a preparation of salivary gland material derived from non-infected Anopheles dirus and profiled for clinical, hematological, functional genomic, lipidomic, proteomic, and metabolomic measurements. Samples were generated and analyzed to investigate the effects of the pharmacological intervention with the anti-malarial drug pyrimethamine on normal individuals. The experiment was designed for 100 days plus a follow-up period, with pyrimethamine administered at three different time points to coincide with the predicted treatment days of experimentally infected rhesus macaques. Capillary blood samples were collected daily for the measurement of CBCs and reticulocytes. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood samples and bone marrow aspirates were collected at seven time points before and after three rounds of drug administration for functional genomic, proteomic, and lipidomic analyses. Within the MaHPIC, this project is known as 'Experiment 13'. This dataset was produced by Dean Jones at Emory University. The following contributed to the creation of this dataset: The MaHPIC Consortium, John Barnwell, Monica Cabrera, Jeremy D. DeBarry, Mary Galinski, Trenton Hoffman, Jay Humphrey, Jianlin Jiang, Chet Joyner, Nicolas Lackman, Stacey Lapp, Esmeralda Meyer, Alberto Moreno, Mustafa Nural, and Suman Pakala. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
INSTITUTE
Emory University
DEPARTMENT
School of Medicine, Vaccine Center at Yerkes
LAST_NAME
Galinksi
FIRST_NAME
Mary
ADDRESS
Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
EMAIL
mahpic@emory.edu
PHONE
none
TOTAL_SUBJECTS
6
STUDY_COMMENTS
31 samples, The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 13' (E13). To access other publicly available results from E13 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public. See Pubmed ID:25453034 for the associated publication for this study.
PGD2 and other lipid mediator changes in mouse adipose associated with administration of an oral inhibitor of H-PGDS (HQL-79)
STUDY_SUMMARY
This is an additional experiment being added onto a previous mouse feeding study that aimed to identify changes in metabolites that occur in metabolic tissues in the obese state that are long-lasting and not reversed by weight loss. We observed in the previous mice feeding study that levels of PGD2 increased in HFD fed mice and stayed high after the diet switch. Other members of the Prostaglandin family followed a similar trend (15-deoxy PGJ2, PGJ2) and were specific to adipose tissue. Based on previously published data indicating that central injection of PGD2 stimulates food intake, we attempted to observe this effect using an oral PGD2 inhibitor of H-PGDS (HQL-79). In fact, the oral inhibitor of the H-PGDS (HQL-79) administered peripherally (oral gavage in mice at 30mg/kg dose) reduced daily food intake. Mice were divided into two groups termed Vehicle (Control) and HGL-79 (H-PGDS inhibitor). Each group was analyzed for lipid mediator changes (including PGD2) in adipose tissue by the Newman lab. Analytical results generally met quality control criterion with respect to surrogate recoveries and replicate precision. Surrogate recoveries were good for most oxylipins (58-76%), endocannabinoids (53-75%), and fatty acids (36%). Recovery precision was good for most analytes in these profiles, ranging from 6-28% RSD for most surrogates. The precision for the LTB4 surrogate was higher than most others (38%). Analytical precision was assessed by duplicate analysis of two separate study samples. Analytical precision was 62 - 69% of analytes having <30% RSD for all profiles and correlation analysis for the analytes within these samples ranged from 0.90-0.99 R2. The complete data set is in the associated excel file (Osborn HQL-79 – Deliverable Data Newman Lab.xls). There were few statistically significant differences observed when comparing concentrations (pmol/gr) between the control and HGL-79 treatment groups. However, when we compared ratios we saw numerous differences between PGD2 and its metabolite d15-PGJ2 versus other prostaglandins. Specifically, ratios between PGD2 and other connected pathway metabolites indicate a shift toward PGE2 and PGF2a production instead of PGD2 (Figure 1) with HQL-79 treatment. The PGD2 and PGE2 metabolites ratio of d15-PGJ2/15-keto PGE2 was statistically significant (P<0.01) using a two-tailed t-test. The ratios of PGD2/PGE2 and PGD2/PGF2 had p values of P<0.09 and P=0.07), respectively. Considering that we were predicting changes that indicated less PGD2 production it may be justifiable to use one-tailed tests instead. In order to maintain consistency with the metabolomic data analysis in the previous study, I followed the same statistical protocol that Johannes preformed for the main Pilot study. Using R and Devium log transformed data. Since this was a two group comparision, if the data was normal a 2 tailed t-test was used and if not normal then Mann-Whitney was used. A far as the significance of a shift from PGD2 to PGE2 production, I found a nice review article that discusses in detail the role of prostaglandins in white adipose tissue (Flachs et al. 2013). In the review it cites articles that have shown PGE2 to induce UCP1, modulate lipolysis adipogenesis, and stimulate leptin release. On the other hand, PGD2 was shown to increase adipogenesis and weight gain. Its downstream product d15-PGJ2 has been shown to increase adipogenesis, adipocyte differentiation, and decrease leptin production. This is significant since I also observed that the ratio of d15-PGJ2 to 15-keto PGE2 (the downstream product of PGE2) was also decreased. Another prostaglandin whose ratio versus PGD2 was different in the inhibitor group was PGF2a which has been shown to increase glucose transport in adipose tissue.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
PGD2 and other lipid mediator changes in mouse adipose associated with administration of an oral inhibitor of H-PGDS (HQL-79)
STUDY_SUMMARY
This is an additional experiment being added onto a previous mouse feeding study that aimed to identify changes in metabolites that occur in metabolic tissues in the obese state that are long-lasting and not reversed by weight loss. We observed in the previous mice feeding study that levels of PGD2 increased in HFD fed mice and stayed high after the diet switch. Other members of the Prostaglandin family followed a similar trend (15-deoxy PGJ2, PGJ2) and were specific to adipose tissue. Based on previously published data indicating that central injection of PGD2 stimulates food intake, we attempted to observe this effect using an oral PGD2 inhibitor of H-PGDS (HQL-79). In fact, the oral inhibitor of the H-PGDS (HQL-79) administered peripherally (oral gavage in mice at 30mg/kg dose) reduced daily food intake. Mice were divided into two groups termed Vehicle (Control) and HGL-79 (H-PGDS inhibitor). Each group was analyzed for lipid mediator changes (including PGD2) in adipose tissue by the Newman lab. Analytical results generally met quality control criterion with respect to surrogate recoveries and replicate precision. Surrogate recoveries were good for most oxylipins (58-76%), endocannabinoids (53-75%), and fatty acids (36%). Recovery precision was good for most analytes in these profiles, ranging from 6-28% RSD for most surrogates. The precision for the LTB4 surrogate was higher than most others (38%). Analytical precision was assessed by duplicate analysis of two separate study samples. Analytical precision was 62 - 69% of analytes having <30% RSD for all profiles and correlation analysis for the analytes within these samples ranged from 0.90-0.99 R2. The complete data set is in the associated excel file (Osborn HQL-79 – Deliverable Data Newman Lab.xls). There were few statistically significant differences observed when comparing concentrations (pmol/gr) between the control and HGL-79 treatment groups. However, when we compared ratios we saw numerous differences between PGD2 and its metabolite d15-PGJ2 versus other prostaglandins. Specifically, ratios between PGD2 and other connected pathway metabolites indicate a shift toward PGE2 and PGF2a production instead of PGD2 (Figure 1) with HQL-79 treatment. The PGD2 and PGE2 metabolites ratio of d15-PGJ2/15-keto PGE2 was statistically significant (P<0.01) using a two-tailed t-test. The ratios of PGD2/PGE2 and PGD2/PGF2 had p values of P<0.09 and P=0.07), respectively. Considering that we were predicting changes that indicated less PGD2 production it may be justifiable to use one-tailed tests instead. In order to maintain consistency with the metabolomic data analysis in the previous study, I followed the same statistical protocol that Johannes preformed for the main Pilot study. Using R and Devium log transformed data. Since this was a two group comparision, if the data was normal a 2 tailed t-test was used and if not normal then Mann-Whitney was used. A far as the significance of a shift from PGD2 to PGE2 production, I found a nice review article that discusses in detail the role of prostaglandins in white adipose tissue (Flachs et al. 2013). In the review it cites articles that have shown PGE2 to induce UCP1, modulate lipolysis adipogenesis, and stimulate leptin release. On the other hand, PGD2 was shown to increase adipogenesis and weight gain. Its downstream product d15-PGJ2 has been shown to increase adipogenesis, adipocyte differentiation, and decrease leptin production. This is significant since I also observed that the ratio of d15-PGJ2 to 15-keto PGE2 (the downstream product of PGE2) was also decreased. Another prostaglandin whose ratio versus PGD2 was different in the inhibitor group was PGF2a which has been shown to increase glucose transport in adipose tissue.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
Dysfunctional lipid metabolism underlies the effect of the perinatal DDT exposure on the development of metabolic syndrome
STUDY_SUMMARY
This study aims to identify changes in lipid mediators in the hypothalamus with triphenyl phosphate (TPP) exposure. UC Davis type 2 diabetes mellitus (UCD-T2DM) rats were treated with TPP (n=8 per group) or not treated (n=8 per group). Each group was analyzed for oxylipin, nitro lipids, endocannabinoid, and endocannabinoid-like monoacylglycerol and N-acylethanolamide changes to investigate alterations in lipid mediator signaling due to TPP exposure. Targeted metabolomic analysis of lipid mediators in rat hypothalamus samples was performed by the Newman lab.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
Dysfunctional lipid metabolism underlies the effect of the perinatal DDT exposure on the development of metabolic syndrome
STUDY_SUMMARY
This study aims to identify changes in lipid mediators in the hypothalamus with triphenyl phosphate (TPP) exposure. UC Davis type 2 diabetes mellitus (UCD-T2DM) rats were treated with TPP (n=8 per group) or not treated (n=8 per group). Each group was analyzed for oxylipin, nitro lipids, endocannabinoid, and endocannabinoid-like monoacylglycerol and N-acylethanolamide changes to investigate alterations in lipid mediator signaling due to TPP exposure. Targeted metabolomic analysis of lipid mediators in rat hypothalamus samples was performed by the Newman lab.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
Metabolomics measures of Macaca mulatta infected with Plasmodium coatneyi Hackeri strain to produce and integrate clinical, hematological, parasitological, and omics measures of acute, recrudescent, and chronic infections.
STUDY_TYPE
Longitudinal parasite infection and treatment of multiple individuals
STUDY_SUMMARY
Malaria-naive male rhesus macaques (Macaca mulatta), approximately four years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered to all subjects at the initial peak of infection, one out of the five macaques received four additional subcurative treatments for subsequent recrudescence peaks. The experimental infection in one subject was ineffective but the macaque was followed-up for the same period of 100 days. The different clinical phases of the infection were clinically determined for each subject. Blood-stage curative doses of artemether were administered to all subjects at the end of the study. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as ‘Experiment 03’. This dataset was produced by Dean Jones at Emory University. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
INSTITUTE
Emory University
DEPARTMENT
School of Medicine, Vaccine Center at Yerkes
LAST_NAME
Galinski
FIRST_NAME
Mary
ADDRESS
Emory University, Yerkes National Primate Research Center, 954 Gatewood Rd, Room 003, Atlanta, GA 30329
EMAIL
mahpic@emory.edu
PHONE
N/A
NUM_GROUPS
6
TOTAL_SUBJECTS
331
STUDY_COMMENTS
The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). Contributors include: Monica Cabrera, Jeremy D. DeBarry, Mary G. Galinski, Jay Humphrey, Dean Jones, Ebru Karpuzoglu, Jessica C. Kissinger, Regina Joice, Esmeralda Meyer, Vishal Nayak, Mustafa Nural, Suman Pakala, ViLinh Tran, Karan Uppal, Loukia Williams. For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 03' (E03). To access other publicly available results from E03 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public.
NEFA Profile Response to Triphenyl Phosphate Exposure
STUDY_SUMMARY
This study aims to identify changes in non-esterified fatty acid (NEFAs) in the plasma with triphenyl phosphate (TPP) exposure. UC Davis type 2 diabetes mellitus (UCD-T2DM) rats were treated with TPP or not treated. Each group was analyzed for non-esterified fatty acid (NEFA) changes to investigate alterations in NEFAs due to TPP exposure. Targeted analysis of NEFA in rat plasma samples was performed by the Newman lab.
INSTITUTE
U.S.D.A. Western Human Nutrition Research Center, University of California, Davis
DEPARTMENT
Nutrition
LAST_NAME
Newman
FIRST_NAME
John
ADDRESS
430 W. Health Sciences Dr., Davis, CA 95616
EMAIL
john.newman@ars.usda.gov
PHONE
+1-530-752-1009
STUDY_COMMENTS
The samples included a high degree of hemolysis exhibited in the plasma. One sample was lost during processing (Group E- Subject 78). Two samples were outliers for multiple analytes and were not included in the final data (E-117 & T-28). Of the samples reported in this data set, there were no missing values.
Untargeted LC-MS metabolomics analysis of human COPD plasma, HILIC & C18
STUDY_SUMMARY
Identify perturbed metabolites and pathways in human plasma collected from 131 COPD subjects. Subjects were either current or former smokers with various COPD phenotypes including emphysema, and exacerbations.
PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association
STUDY_SUMMARY
Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of that can then be used to create a reference library of CCS valuesinformation necessary to create a reference library containing accurate masses, DTIMS arrival times and CCSs for use in high throughput omics analyses. Results: We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software.
Urinary Volatile Compound, Associated with Chronic Inflammation In Interstitial Cystitis
STUDY_SUMMARY
Interstitial cystitis (IC)/bladder pain syndrome (BPS) is a clinical condition that manifests as a sensory hypersensitivity of unknown cause and is characterized by urinary frequency, bladder discomfort, and pelvic pain. In the present volatolomic study, we have analyzed the VOCs unique to urine specimens obtained from interstitial cystitis patients, in compassion to healthy controls.This is the novel finding from comprehensive and unbiased metabolomics analysis that urinary menthol is decreased in urine specimens from IC patients, and that the reduced menthol level in IC is potentially linked to the chronic inflammation, which is often observed in IC patients
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
Impact Of High Sugar Diet On L-Arginine Metabolism In The Lung
STUDY_SUMMARY
Asthma is a progressive inflammatory airways disease that leads to structural airway changes and debilitating symptoms in many severely affected adults. We need novel therapeutic agents that are affordable, can decrease the reliance on steroids, and can improve quality of life. This clinical and mechanistic study has the potential to impact treatment of a subset of adult severe asthmatics and to further our understanding of the mechanisms of L-arginine metabolism and NO biology in the airways of asthmatics. We will pursue a clinical trial in subjects not well controlled on standard drug therapy; this strategy will address whether L-arginine is efficacious in patients receiving standard of care medications. In studies using animal models, we and others have shown that interventions that augment NO levels, through either supplementation of L-arginine or inhibition of arginase, decrease allergic airway inflammation and hyperresponsiveness-the two hallmarks of asthma. Overall, we hypothesize that a responder subset of adult severe asthma patients will derive clinical benefit from supplemental L-arginine therapy and that these patients will have a lower exhaled NO concentrations (<20 ppb) and a higher NOS2/Arg1 mRNA and protein ratio in their airway epithelial cells than non-responders. We aim to: 1) test the hypothesis that uncontrolled, adult severe asthma patients with exhaled breath NO concentrations <20 ppb will have fewer asthma exacerbations over 3 months when treated with L-arginine compared to patients with FeNO > 25, 2) determine the mechanisms by which L-arginine affects the regulation of NOS and arginase enzymes in primary airway epithelial cell cultures from severe asthmatic subjects, and 3) test the hypothesis that inhaled nanoparticle carrier formulations of L-arginine will decrease airway inflammation, airway hyperresponsiveness, and airway fibrosis at lower doses than systemically administered L-arginine. The major impact of our study will be to identify the adult severe asthma cohort that will benefit from supplemental L-arginine therapy. Our ultimate goal is to develop novel therapeutic agents to treat adult severe asthma patients better. PUBLIC HEALTH RELEVANCE: Asthma is a progressive inflammatory airways disease that leads to structural airway changes and debilitating symptoms in many severely affected adults. This clinical study has the potential to improve the care of adult severe asthmatics and to further our understanding of the mechanisms of L-arginine metabolism and nitric oxide biology in the lung. If we demonstrate that L-arginine supplementation can decrease asthma attacks in a subset of severe asthmatics, it will have great implications for future research as well as for the daily lives of patients with asthma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies
STUDY_SUMMARY
The use of dried blood spots (DBS) has many advantages over traditional plasma and serum samples such as the smaller blood volume required, storage at room temperature, and ability to sample in remote locations. However, understanding the robustness of different analytes in DBS samples is essential, especially in older samples collected for longitudinal studies. Here we analyzed the stability of polar metabolites and lipids in DBS samples collected in 2000-2001 and stored at room temperature. The identified and statistically significant molecules were then compared to matched serum samples stored at –80°C to determine if the DBS samples could be effectively used in a longitudinal study following metabolic disease. A total of 400 polar metabolites and lipids were identified in the serum and DBS samples using gas chromatograph/mass spectrometry (GC/MS), liquid chromatography (LC)/MS, and LC/ion mobility spectrometry-MS (LC/IMS-MS). The identified polar metabolites overlapped well between the sample types, though only one statistically significant metabolite was conserved in a case-control study of older diabetic males with low amounts of high-density lipoproteins and high body mass indices, triacylglycerides and glucose levels when compared to non-diabetic patients with normal levels, indicating that degradation in the DBS samples affects polar metabolite quantitation. Differences in the lipid identifications indicated that some oxidation occurs in the DBS samples. However, 36 statistically significant lipids correlated in both sample types. The difference in the number of statistically significant polar metabolites and lipids indicated that the lipids did not degrade to as great of a degree as the polar metabolites in the DBS samples and lipid quantitation was still possible.
LC/MS-MS measurement of inosine to adenosine ratio as well as GC/MS measurement of sarcosine relative values in urine samples from prostate cancer and case control patients in a group of ancestry verified African American and European American.
Sphingolipid Analysis of Human Aqueous Humor in Glaucomatous and Control eyes
STUDY_SUMMARY
This study examined the profiles of sphin¬golipids and ceramides present in the aqueous humor (AH) of human control and POAG donors. Furthermore, we quantitatively compared distinct differences between glaucomatous and age-matched control eyes, identifying potential molecules for further experimentation to determine their biological role in modulating cell behavior. Lipids were identified and ratiometrically quantified in a two-step process using precursor ion scan (PIS) or neutral loss scan (NLS) with appropriate class-specific lipid standards on a TSQ Quantum Access Max mass spectrometer following established procedures. We identified several species of sphingomyelin, sphingoid base, sphingoid base-1-phosphate, and ceramides that were common between control and glaucomatous AQH. Some unique lipid species in these classes were also identified in controls but not in glaucoma and vice versa.
We determined the profiles of sphingomyelin, sphingoid base, sphingoid base-1-phosphate, and ceramide, and their quantitative differences between control and glaucomatous trabecular meshwork (TM) derived from human donors.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
Smoking induced methylation plays a critical role in the accumulation of methylated metabolites, DNA adducts damage and altered metabolism in BCa. These deregulated metabolites can be detected non-invasively and can be used as causal biomarkers that can predict the risk of developing BCa in smokers
GC/MS measurement of sarcosine in urine samples from prostate cancer and case control patients in a group of ancestry verified African American and European Americans.
Human Aqueous Humor Phospholipids in Control and Glaucomatous eyes
STUDY_SUMMARY
An analysis of phospholipid (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine and phosphatidylinositol) classes in human control and glaucomatous aqueous humor (AH). Lipid extraction was performed using a modification of the Bligh and Dyer method, protein concentrations were determined using the Bradford’s method, and select samples were confirmed with Densitometry of PHAST gels. Lipids were identified and subjected to ratiometric quantification using a TSQ Quantum Access Max triple quadrupole mass spectrometer utilizing precursor ion scan (PIS) or neutral ion loss scan (NLS) using appropriate class specific lipid standards in a two-step quantification process. Mass spectrometer data were analyzed using MzMine 2.23.
Validation of the application of targeted metabolomic appraoch in the diagnosis of CFS
STUDY_TYPE
Plasma metabolomic profiling
STUDY_SUMMARY
This study was to validate the utility of the developed targeted metabolomic method in the diagnosis of chronic fatigue syndrome (CFS). Clinical validation consisted of a cohort of 20 male CFS (53 ± 2.8 years old, mean ± SEM, range 21-67 y) and 18 male controls (53 ± 3.5 years old, mean ± SEM, range 23-69 y), who were enrolled in a previous study (Naviaux et al. 2016). These plasma samples were stored in -80 ºC for about 1.5 years and reanalyzed on a different LC-MS/MS system by a different investigator.
INSTITUTE
University of California, San Diego
DEPARTMENT
Department of Medicine
LABORATORY
The Mitochondrial and Metabolic Disease Center
LAST_NAME
Naviaux
FIRST_NAME
Robert
ADDRESS
214 Dikinson Street, CTF-C102, San Diego, CA, 92103
EMAIL
rnaviaux@ucsd.edu
PHONE
619-993-2904
NUM_GROUPS
2
TOTAL_SUBJECTS
38
NUM_MALES
38
STUDY_COMMENTS
These plasma samples were stored in -80 ºC for about 1.5 years and reanalyzed on a different LC-MS/MS system by a different investigator.
Metabolomic Profiling of Follicular Fluid from Patients with Polycystic Ovary Syndrome and Hyper Response to In Vitro Fertilization Treatment
STUDY_TYPE
MS quallitative analysis
STUDY_SUMMARY
The present study consisted in a metabolomic approach in follicular fluid samples from patients with polycystic ovary syndrome and hyper response to in vitro fertilization treatment.
INSTITUTE
Sao Paulo Federal University
DEPARTMENT
Department of Surgery, Division of Urology, Human Reproduction Section
A structural examination and collision cross section database of over 500 metabolities and xenobiotics using drift tube ion mobility
STUDY_TYPE
Library compilation of metabolomic standards
STUDY_SUMMARY
Standards of metabolomic pathways and external secondary metabolites and xenobiotics were analysed with Agilent 6560 Ion mobility QTOF MS platform to build a comprehensive library of Collision Cross Section values. All measurements were performed in triplicate in both positive and negative polarities with nitrogen gas and at seven different electric fields, so that values could be directly measured and random standard deviations (RSD) assessed for each molecule.
INSTITUTE
Pacific Northwest National Laboratory
DEPARTMENT
Integrative Omics
LABORATORY
Pacific Northwest National Laboratory
LAST_NAME
Baker
FIRST_NAME
Erin
ADDRESS
Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA
Sphingolipid Analysis of hyper and normotensive DBA2J mice aqueous humor and trabecular meshwork
STUDY_SUMMARY
To determine the differential profiles of sphingomyelin, sphingoid base, sphingoid base-1-phosphate, and ceramide and their quantitative differences between trabecular meshwork (TM) and aqueous humor (AH) derived from normotensive and hypertensive intraocular pressure states of DBA/2J mice.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
Untargeted metabolomic changes in Chlamydomonas reinhardtii treated with lipid inducing small molecules
STUDY_SUMMARY
A study to investigate the effect of small molecule lipid inducing compounds that leads to hyper accumulation of lipids in N replete cells of Chlamydomonas reinhardtii. These compounds were identified through a high throughput screening designed for that purpose. During that screening, we screened 43,783 compounds and identified 367 primary hits. These 367 hits were further retested using a 8-point dilution series (from 0.25 to 30 uM) and verified the activity of 250 compounds that induce the hyper lipid accumulating phenotype in algae. Once the hit compounds were identified and confirmed, we then performed extensive chemoinformatics analysis to look for common scaffolds and identified several common substructures. We then selected 15 top performing compounds from 5 diverse structural groups and tested biochemical parameters such as growth, lipid accumulating capacity, effect on photosynthetic rates, respiration rates, oxygen consumption rates, analysis of different lipid species to quantify and identify fatty acid species using GC-MS. To understand the global changes in the metabolome, 2 structurally different compounds were selected and compared with cells grown without compounds as control for untargeted metabolomics analysis.
Identification and metabolite profiling of chemical activators of lipid accumulation in green algae
STUDY_TYPE
GC-MS metabolite profiling of algal lipid activators
STUDY_SUMMARY
Microalgae are proposed as feedstock organisms useful for producing biofuels and co-products. However, several limitations must be overcome before algae-based production is economically feasible. Among these is the ability to induce lipid accumulation and storage without affecting biomass yield. To overcome this barrier, a chemical genetics approach was employed in which 43,783 compounds were screened against Chlamydomonas reinhardtii and 243 compounds were identified that increase triacylglyceride (TAG) accumulation without terminating growth. Identified compounds were classified by structural similarity and 15 selected for secondary analyses addressing impacts on growth fitness, photosynthetic pigments, and total cellular protein and starch concentrations. TAG accumulation was verified using GC-MS quantification of total fatty acids and targeted TAG and galactolipid (GL) measurements using LC-MRM/MS. These results demonstrated TAG accumulation does not necessarily proceed at the expense of GL. Untargeted metabolite profiling provided important insights into pathway shifts due to 5 different compound treatments and verified the anabolic state of the cells with regard to the oxidative pentose phosphate pathway, Calvin cycle, tricarboxylic acid cycle and amino acid biosynthetic pathways. Metabolite patterns were distinct from nitrogen starvation and other abiotic stresses commonly used to induce oil accumulation in algae. The efficacy of these compounds was also demonstrated in 3 other algal species. These lipid inducing compounds offer a valuable set of tools for delving into the biochemical mechanisms of lipid accumulation in algae and a direct means to improve algal oil content independent of the severe growth limitations associated with nutrient deprivation.
INSTITUTE
Univ of Nebraska-Lincoln
DEPARTMENT
Biochemistry
LABORATORY
FATTTLab
LAST_NAME
Wase
FIRST_NAME
Nishikant
ADDRESS
1901 Beadle Center, Vine Street, 1901 VINE STREET, Lincoln, NE, 68588-0664, USA
Non-targeted Metabolomics Analysis of Golden Retriever Muscular Dystrophy-Affected Muscles Reveals Alterations in Arginine and Proline Metabolism, and Elevations in Glutamic and Oleic Acid In Vivo
STUDY_SUMMARY
Like Duchenne muscular dystrophy (DMD), the Golden Retriever Muscular Dystrophy (GRMD) dog model of DMD exhibits is characterized by muscle necrosis, progressive paralysis, and pseudohypertrophy in specific skeletal muscles. This severe GRMD phenotype included atrophy of the biceps femoris (BF) and compared to unaffected normal dogs, while the long digital extensor (LDE) of the pelvic limb, serving as a hip flex and stifle extensor, is unaffected. A recent microarray analysis of GRMD identified alterations in genes associated with lipid metabolism and energy production. We, therefore, undertook a non-targeted metabolomics analysis of the GRMD BF (affected) and LDE (unaffected) using GC-MS to identify underlying metabolic defects specific for affected GRMD skeletal muscle. Of the 134 metabolites identified in BF, eight were significantly altered in GRMD BF compared to control BF (Glutamic Acid (2.48 fold vs. controls); Oleic Acid (1.76 fold vs. controls); Proline (1.73 fold vs. controls); Myoinositol-2- Phosphate (0.44 fold vs. controls); Fumaric Acid (0.40 fold vs. controls); Carnosine (0.40 fold vs. controls); Lactamide (0.33 fold vs. controls); and Stearamide (0.23 fold vs. controls). Pathway analysis of the T-test significant metabolites identified BF muscle metabolites significantly enriched for Arginine and proline metabolism (p=5.8E-4, FDR=0.04) and Alanine, aspartate, and glutamate metabolism (p=1.3E-3, FDR=0.05). The GRMD LDE previously reported to be unaffected, in contrast, had only one significantly altered metabolite (3-Phosphoglyceric Acid (0.35 Fold vs. controls)).The identification of elevated BF Oleic acid (a long-chain fatty acid) is consistent with recent microarray studies identifying altered lipid metabolism genes, while alterations in Arginine and Proline metabolism are consistent with recent studies identifying elevated L-arginine in DMD patient sera as a biomarker of disease (alterations in DMD or GRMD muscle itself have not previously been reported).Together, these studies demonstrate muscle-specific alterations in GRMD-affected muscle, which illustrate previously unidentified metabolic changes.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine, Department of Pathology & Laboratory, Department of Pharmacology
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm Road, MBRB 2336, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
(984) 999-5431
STUDY_COMMENTS
Skeletal Muscle (Biceps femoris (BF), long digital extensor(LDE))
Non targeted metabolomic analysis of mouse and human bronchoalveolar lavage fluid, Aqueous(+) experiment (part I)
STUDY_TYPE
Comprehensive profile
STUDY_SUMMARY
Mouse BALF was collected from C57BL/6 mice (n = 10). Five mice were exposed to ambient air for one day (air control) and five mice were exposed to CS for nine months (smoking). Human BALF was collected from subjects from the COPDGene cohort (n = 5). COPD diagnosis was based on the ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1/FVC). Subjects were 45-70 years old, BMI 27-45, weight 76-125kg, and were categorized as follows: 1 male former smoker without COPD (FEV1/FVC = 0.82), 2 male current smokers without COPD (FEV1/FVC = 0.91 and 0.79), 1 female current smoker with moderate COPD (FEV1/FVC = 0.51), and 1 male current smoker with moderate COPD (FEV1/FVC = 0.64).
Non targeted metabolomic analysis of mouse and human bronchoalveolar lavage fluid, Lipid(-) experiment
STUDY_TYPE
Comprehensive profile
STUDY_SUMMARY
Mouse BALF was collected from C57BL/6 mice (n = 10). Five mice were exposed to ambient air for one day (air control) and five mice were exposed to CS for nine months (smoking). Human BALF was collected from subjects from the COPDGene cohort (n = 5). COPD diagnosis was based on the ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1/FVC). Subjects were 45-70 years old, BMI 27-45, weight 76-125kg, and were categorized as follows: 1 male former smoker without COPD (FEV1/FVC = 0.82), 2 male current smokers without COPD (FEV1/FVC = 0.91 and 0.79), 1 female current smoker with moderate COPD (FEV1/FVC = 0.51), and 1 male current smoker with moderate COPD (FEV1/FVC = 0.64)
Non targeted metabolomic analysis of mouse and human bronchoalveolar lavage fluid, Lipid(+) experiment (part III)
STUDY_TYPE
Comprehensive profile
STUDY_SUMMARY
Mouse BALF was collected from C57BL/6 mice (n = 10). Five mice were exposed to ambient air for one day (air control) and five mice were exposed to CS for nine months (smoking). Human BALF was collected from subjects from the COPDGene cohort (n = 5). COPD diagnosis was based on the ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1/FVC). Subjects were 45-70 years old, BMI 27-45, weight 76-125kg, and were categorized as follows: 1 male former smoker without COPD (FEV1/FVC = 0.82), 2 male current smokers without COPD (FEV1/FVC = 0.91 and 0.79), 1 female current smoker with moderate COPD (FEV1/FVC = 0.51), and 1 male current smoker with moderate COPD (FEV1/FVC = 0.64)
TCA Cycle Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine from 20 Participants of the DASH2 Clinical Trial
STUDY_SUMMARY
The objective of the study is to identify changes of urinary metabolite profiles associated with different responses to blood pressure to salt. Subjects are derived from The Dietary approaches to stop hypertension (DASH) diet, Sodium Intake and Blood Pressure Trial (Sacks FM et al PMID: 11136953,N Engl J Med. 2001).We choose two groups subjects who meet the following conditions(the two groups are separately named A and B). We chose subjects on the Control diet .These subjects meet the blood pressure criteria described below:Group A subjects conditions: 1) On Control diet. 2) Normotensive subjects: systolic blood pressure from the low sodium visit is less than 140 and the diastolic blood pressure from low sodium visit is less than 90; 3) For group A: Either the systolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the systolic blood pressure from the low sodium visit, or the diastolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the diastolic blood pressure from the low sodium visit; 3) For group B: The systolic blood pressure from the high sodium visit is within 5 mmHg (i.e. +/- 5) from the systolic blood pressure from the low sodium visit, and the diastolic blood pressure from the high sodium visit is within 5 mmHg from the diastolic blood pressure from the low sodium visit. Use gas chromatography/mass spectrometry (GC/MS) analysis, and liquid chromatography/mass spectrometry (LC/MS)analysis to find the differences of metabolic profiles between the high sodium level and the low sodium level, and compare the metabolic profiles of A with the metabolic profiles of B at the low and high sodium level. Note, this was used as a pilot, the rest of the samples are in another uploaded study.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Amino Acd Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine from 20 Participants of the DASH2 Clinical Trial (part II)
STUDY_SUMMARY
The objective of the study is to identify changes of urinary metabolite profiles associated with different responses to blood pressure to salt. Subjects are derived from The Dietary approaches to stop hypertension (DASH) diet, Sodium Intake and Blood Pressure Trial (Sacks FM et al PMID: 11136953,N Engl J Med. 2001).We choose two groups subjects who meet the following conditions(the two groups are separately named A and B). We chose subjects on the Control diet .These subjects meet the blood pressure criteria described below:Group A subjects conditions: 1) On Control diet. 2) Normotensive subjects: systolic blood pressure from the low sodium visit is less than 140 and the diastolic blood pressure from low sodium visit is less than 90; 3) For group A: Either the systolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the systolic blood pressure from the low sodium visit, or the diastolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the diastolic blood pressure from the low sodium visit; 3) For group B: The systolic blood pressure from the high sodium visit is within 5 mmHg (i.e. +/- 5) from the systolic blood pressure from the low sodium visit, and the diastolic blood pressure from the high sodium visit is within 5 mmHg from the diastolic blood pressure from the low sodium visit. Use gas chromatography/mass spectrometry (GC/MS) analysis, and liquid chromatography/mass spectrometry (LC/MS)analysis to find the differences of metabolic profiles between the high sodium level and the low sodium level, and compare the metabolic profiles of A with the metabolic profiles of B at the low and high sodium level. Note, this was used as a pilot, the rest of the samples are in another uploaded study.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Neuromodulator Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine from 20 Participants of the DASH2 Clinical Trial (part III)
STUDY_SUMMARY
The objective of the study is to identify changes of urinary metabolite profiles associated with different responses to blood pressure to salt. Subjects are derived from The Dietary approaches to stop hypertension (DASH) diet, Sodium Intake and Blood Pressure Trial (Sacks FM et al PMID: 11136953,N Engl J Med. 2001).We choose two groups subjects who meet the following conditions(the two groups are separately named A and B). We chose subjects on the Control diet .These subjects meet the blood pressure criteria described below:Group A subjects conditions: 1) On Control diet. 2) Normotensive subjects: systolic blood pressure from the low sodium visit is less than 140 and the diastolic blood pressure from low sodium visit is less than 90; 3) For group A: Either the systolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the systolic blood pressure from the low sodium visit, or the diastolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the diastolic blood pressure from the low sodium visit; 3) For group B: The systolic blood pressure from the high sodium visit is within 5 mmHg (i.e. +/- 5) from the systolic blood pressure from the low sodium visit, and the diastolic blood pressure from the high sodium visit is within 5 mmHg from the diastolic blood pressure from the low sodium visit. Use gas chromatography/mass spectrometry (GC/MS) analysis, and liquid chromatography/mass spectrometry (LC/MS)analysis to find the differences of metabolic profiles between the high sodium level and the low sodium level, and compare the metabolic profiles of A with the metabolic profiles of B at the low and high sodium level. Note, this was used as a pilot, the rest of the samples are in another uploaded study.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
TCA Cycle Metabolites of Dietary Salt Effects on Blood Pressure in Rat Urine (part IV)
STUDY_SUMMARY
We propose to analyze kidney tissue extract and urine samples from SS and SS.Fh1+ transgenic rats in addition to the analysis of urine samples from the DASH2 trial. The analysis of the rat samples will be highly valuable for several reasons. First, it will to take the findings in human subjects back to animal models and prepare us for further mechanistic studies. We hypothesize at least some of the effects of dietary salt intake on metabolite profiles in human will be recapitulated or altered in the SS rat. If this is confirmed, we will have a highly informative animal model ready for mechanistic studies in which we can investigate the functional contribution of specific metabolites to hypertension and the mechanisms involved. Second, the rat study will allow us to take advantage of a new and unique transgenic SS.Fh1+ model that we recently developed that overexpresses fumarase (Fh1) on the genetic background of the SS rat. Fumarase is a TCA cycle enzyme previously implicated in salt-induced hypertension in SS rats.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Amino Acid Metabolites of Dietary Salt Effects on Blood Pressure in Rat Urine (part V)
STUDY_SUMMARY
We propose to analyze kidney tissue extract and urine samples from SS and SS.Fh1+ transgenic rats in addition to the analysis of urine samples from the DASH2 trial. The analysis of the rat samples will be highly valuable for several reasons. First, it will to take the findings in human subjects back to animal models and prepare us for further mechanistic studies. We hypothesize at least some of the effects of dietary salt intake on metabolite profiles in human will be recapitulated or altered in the SS rat. If this is confirmed, we will have a highly informative animal model ready for mechanistic studies in which we can investigate the functional contribution of specific metabolites to hypertension and the mechanisms involved. Second, the rat study will allow us to take advantage of a new and unique transgenic SS.Fh1+ model that we recently developed that overexpresses fumarase (Fh1) on the genetic background of the SS rat. Fumarase is a TCA cycle enzyme previously implicated in salt-induced hypertension in SS rats.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Neuromodulator Metabolites of Dietary Salt Effects on Blood Pressure in Rat Urine (part VI)
STUDY_SUMMARY
We propose to analyze kidney tissue extract and urine samples from SS and SS.Fh1+ transgenic rats in addition to the analysis of urine samples from the DASH2 trial. The analysis of the rat samples will be highly valuable for several reasons. First, it will to take the findings in human subjects back to animal models and prepare us for further mechanistic studies. We hypothesize at least some of the effects of dietary salt intake on metabolite profiles in human will be recapitulated or altered in the SS rat. If this is confirmed, we will have a highly informative animal model ready for mechanistic studies in which we can investigate the functional contribution of specific metabolites to hypertension and the mechanisms involved. Second, the rat study will allow us to take advantage of a new and unique transgenic SS.Fh1+ model that we recently developed that overexpresses fumarase (Fh1) on the genetic background of the SS rat. Fumarase is a TCA cycle enzyme previously implicated in salt-induced hypertension in SS rats.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
TCA Cycle Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine from DASH2 Clinical Trial (part VII)
STUDY_SUMMARY
The objective of the study is to identify changes of urinary metabolite profiles associated with different responses to blood pressure to salt. Subjects are derived from The Dietary approaches to stop hypertension (DASH) diet, Sodium Intake and Blood Pressure Trial (Sacks FM et al PMID: 11136953,N Engl J Med. 2001).We choose two groups subjects who meet the following conditions(the two groups are separately named A and B). We chose subjects on the Control diet .These subjects meet the blood pressure criteria described below:Group A subjects conditions: 1) On Control diet. 2) Normotensive subjects: systolic blood pressure from the low sodium visit is less than 140 and the diastolic blood pressure from low sodium visit is less than 90; 3) For group A: Either the systolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the systolic blood pressure from the low sodium visit, or the diastolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the diastolic blood pressure from the low sodium visit; 3) For group B: The systolic blood pressure from the high sodium visit is within 5 mmHg (i.e. +/- 5) from the systolic blood pressure from the low sodium visit, and the diastolic blood pressure from the high sodium visit is within 5 mmHg from the diastolic blood pressure from the low sodium visit. Use gas chromatography/mass spectrometry (GC/MS) analysis, and liquid chromatography/mass spectrometry (LC/MS)analysis to find the differences of metabolic profiles between the high sodium level and the low sodium level, and compare the metabolic profiles of A with the metabolic profiles of B at the low and high sodium level.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Amino Acid Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine from DASH2 Clinical Trial (part VIII)
STUDY_SUMMARY
The objective of the study is to identify changes of urinary metabolite profiles associated with different responses to blood pressure to salt. Subjects are derived from The Dietary approaches to stop hypertension (DASH) diet, Sodium Intake and Blood Pressure Trial (Sacks FM et al PMID: 11136953,N Engl J Med. 2001).We choose two groups subjects who meet the following conditions(the two groups are separately named A and B). We chose subjects on the Control diet .These subjects meet the blood pressure criteria described below:Group A subjects conditions: 1) On Control diet. 2) Normotensive subjects: systolic blood pressure from the low sodium visit is less than 140 and the diastolic blood pressure from low sodium visit is less than 90; 3) For group A: Either the systolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the systolic blood pressure from the low sodium visit, or the diastolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the diastolic blood pressure from the low sodium visit; 3) For group B: The systolic blood pressure from the high sodium visit is within 5 mmHg (i.e. +/- 5) from the systolic blood pressure from the low sodium visit, and the diastolic blood pressure from the high sodium visit is within 5 mmHg from the diastolic blood pressure from the low sodium visit. Use gas chromatography/mass spectrometry (GC/MS) analysis, and liquid chromatography/mass spectrometry (LC/MS)analysis to find the differences of metabolic profiles between the high sodium level and the low sodium level, and compare the metabolic profiles of A with the metabolic profiles of B at the low and high sodium level.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Neuromodulator Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine from DASH2 Clinical Trial (part IX)
STUDY_SUMMARY
The objective of the study is to identify changes of urinary metabolite profiles associated with different responses to blood pressure to salt. Subjects are derived from The Dietary approaches to stop hypertension (DASH) diet, Sodium Intake and Blood Pressure Trial (Sacks FM et al PMID: 11136953,N Engl J Med. 2001).We choose two groups subjects who meet the following conditions(the two groups are separately named A and B). We chose subjects on the Control diet .These subjects meet the blood pressure criteria described below:Group A subjects conditions: 1) On Control diet. 2) Normotensive subjects: systolic blood pressure from the low sodium visit is less than 140 and the diastolic blood pressure from low sodium visit is less than 90; 3) For group A: Either the systolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the systolic blood pressure from the low sodium visit, or the diastolic blood pressure from the high sodium visit was greater than 10 mmHg higher than the diastolic blood pressure from the low sodium visit; 3) For group B: The systolic blood pressure from the high sodium visit is within 5 mmHg (i.e. +/- 5) from the systolic blood pressure from the low sodium visit, and the diastolic blood pressure from the high sodium visit is within 5 mmHg from the diastolic blood pressure from the low sodium visit. Use gas chromatography/mass spectrometry (GC/MS) analysis, and liquid chromatography/mass spectrometry (LC/MS)analysis to find the differences of metabolic profiles between the high sodium level and the low sodium level, and compare the metabolic profiles of A with the metabolic profiles of B at the low and high sodium level.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
TCA Cycle Metabolites of Dietary Salt Effects on Blood Pressure in Rat Urine and Kidney Tissue (part X)
STUDY_SUMMARY
We propose to analyze kidney tissue extract and urine samples from SS and SS.Fh1+ transgenic rats in addition to the analysis of urine samples from the DASH2 trial. The analysis of the rat samples will be highly valuable for several reasons. First, it will to take the findings in human subjects back to animal models and prepare us for further mechanistic studies. We hypothesize at least some of the effects of dietary salt intake on metabolite profiles in human will be recapitulated or altered in the SS rat. If this is confirmed, we will have a highly informative animal model ready for mechanistic studies in which we can investigate the functional contribution of specific metabolites to hypertension and the mechanisms involved. Second, the rat study will allow us to take advantage of a new and unique transgenic SS.Fh1+ model that we recently developed that overexpresses fumarase (Fh1) on the genetic background of the SS rat. Fumarase is a TCA cycle enzyme previously implicated in salt-induced hypertension in SS rats.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Amino Acid Metabolites of Dietary Salt Effects on Blood Pressure in Rat Urine and Kidney Tissue (part I)
STUDY_SUMMARY
We propose to analyze kidney tissue extract and urine samples from SS and SS.Fh1+ transgenic rats in addition to the analysis of urine samples from the DASH2 trial. The analysis of the rat samples will be highly valuable for several reasons. First, it will to take the findings in human subjects back to animal models and prepare us for further mechanistic studies. We hypothesize at least some of the effects of dietary salt intake on metabolite profiles in human will be recapitulated or altered in the SS rat. If this is confirmed, we will have a highly informative animal model ready for mechanistic studies in which we can investigate the functional contribution of specific metabolites to hypertension and the mechanisms involved. Second, the rat study will allow us to take advantage of a new and unique transgenic SS.Fh1+ model that we recently developed that overexpresses fumarase (Fh1) on the genetic background of the SS rat. Fumarase is a TCA cycle enzyme previously implicated in salt-induced hypertension in SS rats.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Neuromodulator Metabolites of Dietary Salt Effects on Blood Pressure in Rat Urine and Kidney Tissue (part XII)
STUDY_SUMMARY
We propose to analyze kidney tissue extract and urine samples from SS and SS.Fh1+ transgenic rats in addition to the analysis of urine samples from the DASH2 trial. The analysis of the rat samples will be highly valuable for several reasons. First, it will to take the findings in human subjects back to animal models and prepare us for further mechanistic studies. We hypothesize at least some of the effects of dietary salt intake on metabolite profiles in human will be recapitulated or altered in the SS rat. If this is confirmed, we will have a highly informative animal model ready for mechanistic studies in which we can investigate the functional contribution of specific metabolites to hypertension and the mechanisms involved. Second, the rat study will allow us to take advantage of a new and unique transgenic SS.Fh1+ model that we recently developed that overexpresses fumarase (Fh1) on the genetic background of the SS rat. Fumarase is a TCA cycle enzyme previously implicated in salt-induced hypertension in SS rats.
INSTITUTE
Mayo Clinic
LAST_NAME
Liang
FIRST_NAME
Mingyu
ADDRESS
Medical College of Wisconsin 8701 Watertown Plank Road Milwaukee, WI 53226
Targeted NEFA in American Indian Adolescents (part I)
STUDY_SUMMARY
The goal of this study is to determine the effect of physical activity on the blood concentrations of several compounds that are proposed to be markers of diabetic risk. We will compare results from normal weight and obese American Indian adolescents, with high or low habitual physical activity. We will also compare the same blood markers in the obese group before and after 4 months of exercise to measure the benefit of the program.
INSTITUTE
Mayo Clinic
LAST_NAME
Short
FIRST_NAME
Kevin
ADDRESS
University of Oklahoma Health Sciences Center 1200 Children’s Ave, Suite 4500 Oklahoma City, OK 73104
Targeted Amino Acids in American Indian Adolescents (part II)
STUDY_SUMMARY
The goal of this study is to determine the effect of physical activity on the blood concentrations of several compounds that are proposed to be markers of diabetic risk. We will compare results from normal weight and obese American Indian adolescents, with high or low habitual physical activity. We will also compare the same blood markers in the obese group before and after 4 months of exercise to measure the benefit of the program.
INSTITUTE
Mayo Clinic
LAST_NAME
Short
FIRST_NAME
Kevin
ADDRESS
University of Oklahoma Health Sciences Center 1200 Children’s Ave, Suite 4500 Oklahoma City, OK 73104
Effects of Exercise on Dystrophic Mouse Muscle Amino Acids (part II)
STUDY_SUMMARY
We will use male C57BL10, mdx, and nNOS-/- mice (n = 10 each group) to characterize the skeletal and cardiac muscle metabolomes. Half of the mice in each group will remain sedentary while the other half will be subjected to a single bout of treadmill exercise to exhaustion. Mice will be euthanized immediately postexercise and blood, hearts, and hindlimb muscles will be harvested and frozen as detailed in the General Methods. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of Exercise on Dystrophic Mouse Muscle TCA Cycle (part II)
STUDY_SUMMARY
We will use male C57BL10, mdx, and nNOS-/- mice (n = 10 each group) to characterize the skeletal and cardiac muscle metabolomes. Half of the mice in each group will remain sedentary while the other half will be subjected to a single bout of treadmill exercise to exhaustion. Mice will be euthanized immediately postexercise and blood, hearts, and hindlimb muscles will be harvested and frozen as detailed in the General Methods. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of Exercise on Dystrophic Mouse Muscle Non-Esterified Fatty Acids (part III)
STUDY_SUMMARY
We will use male C57BL10, mdx, and nNOS-/- mice (n = 10 each group) to characterize the skeletal and cardiac muscle metabolomes. Half of the mice in each group will remain sedentary while the other half will be subjected to a single bout of treadmill exercise to exhaustion. Mice will be euthanized immediately postexercise and blood, hearts, and hindlimb muscles will be harvested and frozen as detailed in the General Methods. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of NO Donor Therapy on the Dystrophic Mouse Muscle Amino Acids (part IV)
STUDY_SUMMARY
For this aim, we will only use male mdx mice. We will study three groups treated for 7 days with vehicle, naproxcinod (i.e., NO-naproxen), or naproxen (n = 10 each group). Two hours after the final treatment, half the mice in each group will be run to exhaustion on a treadmill. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of NO Donor Therapy on the Dystrophic Mouse Muscle Non-Esterified Fatty Acids (part V)
STUDY_SUMMARY
For this aim, we will only use male mdx mice. We will study three groups treated for 7 days with vehicle, naproxcinod (i.e., NO-naproxen), or naproxen (n = 10 each group). Two hours after the final treatment, half the mice in each group will be run to exhaustion on a treadmill. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of NO Donor Therapy on the Dystrophic Mouse Muscle TCA Cycle (part VI)
STUDY_SUMMARY
For this aim, we will only use male mdx mice. We will study three groups treated for 7 days with vehicle, naproxcinod (i.e., NO-naproxen), or naproxen (n = 10 each group). Two hours after the final treatment, half the mice in each group will be run to exhaustion on a treadmill. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of NO Donor Therapy on the Dystrophic Mouse Heart Metabolome (part VII)
STUDY_SUMMARY
For this aim, we will only use male mdx mice. We will study three groups treated for 7 days with vehicle, naproxcinod (i.e., NO-naproxen), or naproxen (n = 10 each group). Two hours after the final treatment, half the mice in each group will be run to exhaustion on a treadmill. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS).
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of NO Donor Therapy on the Dystrophic Mouse Quadricep Metabolome (part VIII)
STUDY_SUMMARY
For this aim, we will only use male mdx mice. We will study three groups treated for 7 days with vehicle, naproxcinod (i.e., NO-naproxen), or naproxen (n = 10 each group). Two hours after the final treatment, half the mice in each group will be run to exhaustion on a treadmill. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS).
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of Exercise on Dystrophic Mouse Heart Meabolome (part IX)
STUDY_SUMMARY
We will use male C57BL10, mdx, and nNOS-/- mice (n = 10 each group) to characterize the skeletal and cardiac muscle metabolomes. Half of the mice in each group will remain sedentary while the other half will be subjected to a single bout of treadmill exercise to exhaustion. Mice will be euthanized immediately postexercise and blood, hearts, and hindlimb muscles will be harvested and frozen as detailed in the General Methods. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Effects of Exercise on Dystrophic Mouse Quadricep Meabolome (part X)
STUDY_SUMMARY
We will use male C57BL10, mdx, and nNOS-/- mice (n = 10 each group) to characterize the skeletal and cardiac muscle metabolomes. Half of the mice in each group will remain sedentary while the other half will be subjected to a single bout of treadmill exercise to exhaustion. Mice will be euthanized immediately postexercise and blood, hearts, and hindlimb muscles will be harvested and frozen as detailed in the General Methods. The heart and gastrocnemius, soleus, and quadriceps muscles of one hindlimb will be sent to the Mayo Clinic Metabolomics Resource Core. The heart and quadriceps muscle will be used for untargeted metabolomics profiling (LC/MS) while the gastrocnemius and soleus muscles will be used for targeted analyses of amino acids plus amino metabolites, non-esterified fatty acids, and citric acid cycle intermediates.
INSTITUTE
Mayo Clinic
LAST_NAME
Thomas
FIRST_NAME
Gail
ADDRESS
Penn State Hershey Heart and Vascular Institute Penn State College of Medicine 500 University Drive, MC H047 Hershey, PA 17033
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice (part II)
STUDY_SUMMARY
In this study we have compared the metabolic effects of conventional soybean oil to those of genetically modified Plenish soybean oil, that is low in linoleic acid and high in oleic acid. This work builds on our previous study showing that soybean oil, rich in polyunsaturated fats, is more obesogenic and diabetogenic than coconut oil, rich in saturated fats (PMID: 26200659). Here, in order to elucidate the mechanisms responsible for soybean oil induced obesity, we have performed the first ever metabolomics (in plasma and liver) and proteomics on the livers of mice fed the two soybean oil diets (plus those fed a high coconut oil and Viv chow diet). Our results show that the new high oleic soybean oil induces less obesity and adiposity than conventional soybean oil, but can cause hepatomegaly and liver dysfunction. Metabolomic analysis reveals that the hepatic and plasma metabolic profiles differ considerably between the two soybean oils. Hepatic C18 oxylipin metabolites of omega-6 (ω6) and omega-3 (ω3) fatty acids (linoleic and α-linolenic acid, respectively) in the cytochrome P450/soluble epoxide hydrolase pathway were found to correlate positively with obesity.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice (part III)
STUDY_SUMMARY
In this study we have compared the metabolic effects of conventional soybean oil to those of genetically modified Plenish soybean oil, that is low in linoleic acid and high in oleic acid. This work builds on our previous study showing that soybean oil, rich in polyunsaturated fats, is more obesogenic and diabetogenic than coconut oil, rich in saturated fats (PMID: 26200659). Here, in order to elucidate the mechanisms responsible for soybean oil induced obesity, we have performed the first ever metabolomics (in plasma and liver) and proteomics on the livers of mice fed the two soybean oil diets (plus those fed a high coconut oil and Viv chow diet). Our results show that the new high oleic soybean oil induces less obesity and adiposity than conventional soybean oil, but can cause hepatomegaly and liver dysfunction. Metabolomic analysis reveals that the hepatic and plasma metabolic profiles differ considerably between the two soybean oils. Hepatic C18 oxylipin metabolites of omega-6 (ω6) and omega-3 (ω3) fatty acids (linoleic and α-linolenic acid, respectively) in the cytochrome P450/soluble epoxide hydrolase pathway were found to correlate positively with obesity.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
mTOR regulates metabolic adaptation of APCs in the lung microenvironment and controls the outcome of allergic inflammation
STUDY_SUMMARY
Antigen presenting cells (APCs) occupy diverse anatomical tissues, but their tissue-restricted homeostasis remains poorly understood. Here, working in mouse models of inflammation, we found that mTOR-dependent metabolic adaptation was required at discrete locations. mTOR was dispensable for DC homeostasis in secondary lymphoid tissues, but necessary to regulate cellular metabolism and accumulation of CD103+ DCs and alveolar macrophages in lung. Moreover, whilst numbers of mTOR-deficient lung CD11b+ DCs were not changed, they were metabolically reprogrammed to skew allergic inflammation from eosinophilic Th2 to neutrophilic Th17 polarity. The mechanism for this change was independent of translational control, but dependent on inflammatory DC which produced IL-23 and increased fatty acid oxidation. mTOR therefore mediates metabolic adaptation of APCs in distinct tissues, influencing the immunological character of allergic inflammation.
INSTITUTE
Emory University
LAST_NAME
Li; Gardinassi
FIRST_NAME
Shuzhao; Luiz
ADDRESS
Emory Woodruff Memorial Research Building, 1639 Pierce Dr NE, Atlanta, GA 30322
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice (part IV)
STUDY_SUMMARY
In this study we have compared the metabolic effects of conventional soybean oil to those of genetically modified Plenish soybean oil, that is low in linoleic acid and high in oleic acid. This work builds on our previous study showing that soybean oil, rich in polyunsaturated fats, is more obesogenic and diabetogenic than coconut oil, rich in saturated fats (PMID: 26200659). Here, in order to elucidate the mechanisms responsible for soybean oil induced obesity, we have performed the first ever metabolomics (in plasma and liver) and proteomics on the livers of mice fed the two soybean oil diets (plus those fed a high coconut oil and Viv chow diet). Our results show that the new high oleic soybean oil induces less obesity and adiposity than conventional soybean oil, but can cause hepatomegaly and liver dysfunction. Metabolomic analysis reveals that the hepatic and plasma metabolic profiles differ considerably between the two soybean oils. Hepatic C18 oxylipin metabolites of omega-6 (ω6) and omega-3 (ω3) fatty acids (linoleic and α-linolenic acid, respectively) in the cytochrome P450/soluble epoxide hydrolase pathway were found to correlate positively with obesity.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Changes in metabolites and lipid mediators associated with supervised exercise training for peripheral
STUDY_TYPE
Timecourse
STUDY_SUMMARY
Peripheral artery disease (PAD) is a leading cause of cardiovascular related morbidity and mortality, affecting over 8.5 million men and women in the United States and greater than 200 million individuals worldwide. The mainstay of treatment to improve lower limb symptoms is supervised walking therapy, which does not affect plaque morphology or alter conduit artery blood flow, but rather ameliorates endothelial dysfunction, enhances skeletal muscle metabolism and mitochondrial function, and suppresses inflammatory activation. In this pilot feasibility project we will employ metabolic and lipidomic techniques to measure the effects of supervised exercise therapy on primary metabolism, complex lipids, and lipid mediators, and correlate these effects with individual, subject-level measures of the response to exercise therapy among subjects with PAD. The overarching theme of this work is to identify metabolites, complex lipids, and lipid mediators that are associated with the inter-individual variability in the response of subjects with PAD to supervised exercise therapy. This knowledge will significantly enhance our understanding of the pathophysiology of lower extremity symptoms in PAD, as well as the manner in which supervised exercise therapy improves walking intolerance. It will identify novel therapeutic targets and pathways for pharmacologic manipulation in the treatment of PAD. Aside from having the potential to generate multiple high-impact publications, it will serve as the basis for a planned NIH R01 submission by the PI at the conclusion of the award period.
INSTITUTE
USDA
DEPARTMENT
Obesity and metabolism research unit
LAST_NAME
Newman
FIRST_NAME
John
ADDRESS
430 West Health Sciences Dr. Davis, Ca, 95616
EMAIL
john.newman@ars.usda.gov
PHONE
(530) 752-1009
STUDY_COMMENTS
Fatty acids measured but not against a calibration curve. Therefore values are expressed as a relative abundance of the entire samples set such that the sum of all subjects eguals 100%.
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice (part I)
STUDY_SUMMARY
In this study we have compared the metabolic effects of conventional soybean oil to those of genetically modified Plenish soybean oil, that is low in linoleic acid and high in oleic acid. This work builds on our previous study showing that soybean oil, rich in polyunsaturated fats, is more obesogenic and diabetogenic than coconut oil, rich in saturated fats (PMID: 26200659). Here, in order to elucidate the mechanisms responsible for soybean oil induced obesity, we have performed the first ever metabolomics (in plasma and liver) and proteomics on the livers of mice fed the two soybean oil diets (plus those fed a high coconut oil and Viv chow diet). Our results show that the new high oleic soybean oil induces less obesity and adiposity than conventional soybean oil, but can cause hepatomegaly and liver dysfunction. Metabolomic analysis reveals that the hepatic and plasma metabolic profiles differ considerably between the two soybean oils. Hepatic C18 oxylipin metabolites of omega-6 (ω6) and omega-3 (ω3) fatty acids (linoleic and α-linolenic acid, respectively) in the cytochrome P450/soluble epoxide hydrolase pathway were found to correlate positively with obesity.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Evaluation of plasma samples from the CHOICE clinical weight loss study in which obese post menopausal breast cancer survivors lost >15% initial body weight following either a low carbohydrate or a low fat dietary pattern. These samples will be interrogated for changes in metabolic intermediates and lipid metabolites that may be indicative of changes in prognosis for long term survival following treatment for breast cancer. Samples will be subjected to LCMS and shotgun lipidomics. In parallel, plasma and mammary gland fat pad from an obese rat model for breast cancer in which rats were subjected to a parallel level of weight loss will also be interrogated using the same procedures in an effort to inform the interpretation of the clinical data.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The samples are frozen biopsies of whilte subcutaneous adipose tissues (50 mg). Samples were collected from 4 hormone-sensitive lipase (HSL) WT patients (adipose insulin sensitive), 3 HSL heterozygote patients and 1 HSL KO patient.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
These are fasted plasma samples collected from bipolar and control subjects following a 7-day diet journaling period. The purpose of the experiment is to evaluate potential differences in lipid concentrations/metabolism between bipolar and control subjects with the ability to correct for dietary intake, age, gender and medication use.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Rats were subjected to bilateral rotator cuff tears of the right and left supraspinatus muscle. Muscles were harvested from each shoulder at 0, 10, 30, or 60 days post surgery.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Determining lipid composition of diabetic microvascular complication-prone tissues and comparing tissues levels to plasma levels. Samples are in addition to plasma and kidney tissue samples ran (shotgun lipidomics) in June-July 2014.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Subjects were subjected to different dietary interventions. Indivduals (A1 to A19) were either randomized to a isocaloric diet with either 40-45% saturated fat diet or 40-45% monounsaturated fat diet for 4 weeks. Plasma was sampled at baseline and after 4 weeks on the diet in the fasting state. Multiple clinical values (Weight, blood pressure, pulse,total cholesterol, HDL, LDL and triglycerides) and hyperinsulinemic euglycemic clamps were assessed. Alternatively (XS-3 to XS 43) were provided a diet that was 2000 calories above the estimated isocaloric state for 2 weeks. Multiple clinical values (Weight, blood pressure, pulse,total cholesterol, HDL, LDL and triglycerides) were determined along with body composition, insulin and glucose values.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Characterization of Retinal Exudates in Coats Disease - lipid profile
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The aim of our study is to characterize the retinal lipid exudates through lipidomic assays. Lipidomic analysis will quantify and identify the retinal lipid exudates and provide a `lipid profile? of the exudates. The characterization of the retinal lipids will help in further understanding the pathogenesis of Coat?s disease. It may allow us to identify and therapeutically target a metabolic pathway to prevent retinal exudation abnormal in Coat?s disease.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Wild type (a/a) agouti mouse dams were randomized to one of three diets (control, mediterranean, western) two weeks prior to pairing with an agouti (Avy/a) sire. Diet exposure continued through pregnancy and lactation. All pups were weaned onto the control diet and then followed for metabolic phenotyping measures to 10 months of age. Comprehensive phenotyping (body composition, CLAMS, blood draw) was completed at 2, 4, and 8 months, with an OGTT at 8 months. Weekly weights were also recorded. The study examines whether prenatal dietary exposure to high fat diets (HFD) and bisphenol a (BPA, those groups will not be tested in this pilot) impacts metabolic programming in offspring as measured by hepatic steatosis, serum hormone levels, and epigenetic changes in hepatic lipid metabolism genes.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
8
TOTAL_SUBJECTS
6
STUDY_COMMENTS
Shotgun lipidomics will add insight into the potentially changing lipid composition of membranes in offspring following different prenatal diet exposures as a means of assessing risk of steatosis and metabolic changes.
LCR and HCR rats (from Nathan Qi's 2010 study) were dissected at rest or following 10 minutes of exercise. Mitochondria were isolated from frozen gastrocnemius skeletal muscle. Samples consist of these isolated mitochondria suspended in 50 uL of mitochondrial isolation buffer (IBM containing sucrose, salts, etc; see Katie Overmyer's notebook E, p~23).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
4
TOTAL_SUBJECTS
12
STUDY_COMMENTS
Recommend extracting entire sample suspension, NOT pelleting and removing supernatant. Quantities are likely to be small (~1-3mg tissue each?) Protein assays were performed to estimate quantities; see Katie's notebook or contact Charles for these protein concentration estimates, but also RECOMMEND SAVING RESIDUAL PELLET to allow further normalization.
Plasma, kidney, sciatic nerve, and retina samples collected from control (db/m) and diabetic (db/db) mice. Samples snap frozen and stored at -80. Plasma volume measured and tissues weighed for lipid extraction.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
6
TOTAL_SUBJECTS
31
STUDY_COMMENTS
Plasma and kidney samples were originally prepped in June 2014 and analyzed on our first TripleTOF. George Michailidis has requested they be re-analyzed to compare results between platforms. N/R #91-111 are new samples that will be prepared for this experiment (n = 40). WHEN ANALYZING: need to separate by tissue (P, K, N, R) for imputation of missing values. Want raw data and normalized to IS.
The mice were injected via tail vein with either shBmal1 adenovirus or shLacz adenocirus as control (n=5 for each group), following 10 days of 5% ethanol diet feeding. Then the mice were dissected and liver tissues were flash freezed. 25mg liver tissues from each mouse of the same group were pooled.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effects of rosiglitazone treatment on lipid composition
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Reprograming of 'white' to 'brite' adipocytes with higher oxidative capacity and improved endocrine function represents a potentially important approach to address the dysfunctional adipocyte phenotypes in obesity. We find that chronic treatment with the PPAR? agonist (rosiglitazone, 1 uM for 7days in vitro) in white human adipose tissue induced metabolic changes. Our trancriptome analysis showed that higher mitochondrial and peroxisomal fatty acid oxidation pathways and other genes involved in lipid metabolism including (re)esterification are induced by rosiglitazone treatment. To understand the biochemical basis of brite vs. white human adipocytes, we will perform comprehensive metabolomic profiling of control and rosiglitazone treated tissues using unbiased lipidomics approach.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effect of high fat diet and streptozotocin treatment on neuropathy
STUDY_TYPE
MS analysis
STUDY_SUMMARY
C57BL6 male mice were fed either a control 10% fat (RD D12540-B) or a high fat 60% fat (RD 12492) diet from 5 wk age. STZ was given to some groups at 12 wk age. Chow was reversed in some groups (DR) from 60% HF to 10 % HF at 16 wk age. Mice were euthanized at either 16 wk or 24 wk age. Neuropathy phenotyping occured prior to all harvests.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Nonalcoholic steatohepatitis (NASH) changes with S.Q. Leptin administrations
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Samples are from individuals with documented fatty liver disease (NAFLD) from whom serum was drawn at baseline and after 1 and 12 months of S.Q. Leptin administrations. The effect of leptin on degree of steatosis and inflammation was assessed in liver biopsies at baseline and following 1 year of treatment.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Functional genomics study on Non Alcoholic fatty liver disease (NAFLD)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
In this experiment, vector , GCKR (WT), GCKR(P446L), PPP1R3B, TM6SF2 (WT and E167K) overexpression stable HuH-7_Lok cell lines as well as Non-target, GCKR shRNA (52621), PPP1R3B shRNA (2640), TM6SF2 shRNA (382426) knockdown HuH-7_Lok cell lines are used to do the lipidomics experiments 3 X 100 mm dishes of cells were seeded (1x106 cells/dish) for each cell line and incubated at 37? C for 24 hours, then replaced medium with delipidated serum DMEM medium. After 24 hours, treated with BSA-OA (200?M) for another 24 hours before the collection of cells Add 4mL/dish 50 mM ammonium acetate wash cells and then quench cells by adding liquid nitrogen covering all the surface of dish. Store the cell samples in -80?C freezer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part II
STUDY_TYPE
MS analysis
STUDY_SUMMARY
In this experiment, vector , GCKR (WT), GCKR(P446L), PPP1R3B, TM6SF2 (WT and E167K) overexpression stable HuH-7_Lok cell lines as well as Non-target, GCKR shRNA (52621), PPP1R3B shRNA (2640), TM6SF2 shRNA (382426) knockdown HuH-7_Lok cell lines are used to do the lipidomics experiments 3 X 100 mm dishes of cells were seeded (1x106 cells/dish) for each cell line and incubated at 37? C for 24 hours, then replaced medium with delipidated serum DMEM medium. After 24 hours, treated with BSA-OA (200?M) for another 24 hours before the collection of cells Add 4mL/dish 50 mM ammonium acetate wash cells and then quench cells by adding liquid nitrogen covering all the surface of dish. Store the cell samples in -80?C freezer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part III
STUDY_TYPE
MS analysis
STUDY_SUMMARY
In this experiment, vector , GCKR (WT), GCKR(P446L), PPP1R3B, TM6SF2 (WT and E167K) overexpression stable HuH-7_Lok cell lines as well as Non-target, GCKR shRNA (52621), PPP1R3B shRNA (2640), TM6SF2 shRNA (382426) knockdown HuH-7_Lok cell lines are used to do the lipidomics experiments 3 X 100 mm dishes of cells were seeded (1x106 cells/dish) for each cell line and incubated at 37? C for 24 hours, then replaced medium with delipidated serum DMEM medium. After 24 hours, treated with BSA-OA (200?M) for another 24 hours before the collection of cells Add 4mL/dish 50 mM ammonium acetate wash cells and then quench cells by adding liquid nitrogen covering all the surface of dish. Store the cell samples in -80?C freezer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
ARetinal tissue knockout to study efflux of cholesterol (AGCA1/G1 double KO - TY and LysM cre)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
ABCA1 and AGCG1, which is important gene to efflux the cholesterol from the cell/tissue, are knocked out in specific retinal tissue. T:RPE specific, L:macrophage specific.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Retinal tissue knockout to study efflux of cholesterol (AGCA1/G1 double KO - TY and LysM cre) - part II
STUDY_TYPE
MS analysis
STUDY_SUMMARY
ABCA1 and AGCG1, which is important gene to efflux the cholesterol from the cell/tissue, are knocked out in specific retinal tissue. R:Rod specific, C:Cone specific.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Untargeted Lipidomics for hepatic lipid profile wild type versus knockout
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Use untargeted lipidomics to investigate differences in hepatic lipid profile between wild type and knockout mice. Mice were fed with high fat diet for 10 weeks and sacrificed under randomly fed condition. Liver were harvested freshly and frozen into liquid nitrogen immediately. Each sample was combined liver tissues from three individual mice in the same group.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effect of fatty acids on macrophage (wild type versus knockout) lipid levels
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Macrophages from wild type or knockout mice with various treatments [none, BSA (control), palmitate + oleate, conditioned media from adipocytes treated with either BSA or palmitate + oleate). N=4/group.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
On day 1, seed 1 million cells/dish Huh7_Lok cells (vector, GCKR(WT), GCKR(P446L), Non-Target, GCKR KD and PPP1R3B/OE) in 100 mm dishes with DMEM complete medium and incubate at 37C for 24 h. On day 2, replace DMEM medium with delipidated serum medium for these cells and incubate for another 24 h. On day 3, add heated Oleic Acid-Albumin into each dish at final concentration of 200?M for 24h. On day 4, collect cells with Trypsin/EDTA lysis and count cells with automated cell counter and calculate total cell numbers in each sample, then centrifuge cells down and take out the supernatant and keep cells in -80 C freezer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Lipodomics and Gestational bisphenol A (BPA) exposure
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Gestational BPA exposure in sheep induces metabolic phenotype in sheep characterized by peripheral insulin resistance and increased adipocyte size. Because insulin sensitivity can be regulated by various agents including free fatty acids (FFA), we hypothesize that gestational BPA exposure alters circulating FFA inducing dyslipidemia, a marker of metabolic disorder. Because saturated FFA is associated with insulin resistance, determination of the FFA profile in these species aid in understanding the underlying mechanism. Additionally, because of the non-monotonic nature of responses to BPA exposure dose response studies are also needed. This study will therefore assess plasma lipid profile in sheep exposed to three different doses of BPA prenatally and compared with untreated control animals
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
4
TOTAL_SUBJECTS
28
STUDY_COMMENTS
Metabolic disorders such as obesity and diabetes are currently widespread with epidemic proportions. Recent studies have implicated that these disorders have developmental basis due to maternal exposure to adverse insults including endocrine disruptors such as Bisphenol A (BPA). As BPA is present in maternal serum, amniotic fluid, cord blood taken at birth, placenta, colostrum and breast milk suggests that BPA has developmental impacts. In fact developmental BPA exposure have been linked to intrauterine growth restriction and low birth weight offspring, risk factors for adult cardiometabolic abnormalities. Animal models are helpful to study the effect of developmental BPA exposure and determine associated mechanisms.
Biomarkers for different types of Multiple Scelerosis (MS) (BMS vs SPMS lipidomics)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Metabolomic Analysis in Secondary Progressive and Benign MS. Preliminary data: We have conducted whole blood cell microarray comparing gene expression profile of 20 SPMS and 13 BMS patients. The data revealed significant increase in pathways involving iron ion binding, oxygen transporter activity and hemoglobin functions. Specifically, the identified down regulated genes are involved in interacting selectively and non-covalently with iron (Fe) ions. Heme has been described as a potent pro-inflammatory molecule that can induce multiple innate immune responses, and cause excessive iron and heme-induced oxidative stress and cell death. In the brain, it causes neurodegeneration. In addition, our microarray preliminary results also show a statistically significant increase in arachidonate 12-lipoxygenase activity in SPMS compared to benign MS. Specific aim. To validate metabolites and lipid biomarkers in serum samples from patients with benign and secondary progressive MS. Our central hypothesis is that the gene expression in various types of multiple sclerosis likely create a systematic metabolomic/lipidomic environment that leads to progression in MS. We plan to compare and contrast metabolomics in SP-MS to BMS patients using the innovative technology at the Metabolomics Research Core at the University of Michigan. By monitoring lipid and metabolite changes in SP and BMS patients, we aim to identify molecular processes and biomarkers of axonal damage for MS. Then, we plan to translate such metabolomic biomarkers to correlate with our rich clinical, immunological and imaging readouts. The goal of this project is to develop a blood-based test to differentiate SP-MS from BMS patients. To accomplish this, we will first identify the gene expression signature associated with of SP-MS. Then, we will correlate these gene expression changes with lipids and metabolite changes in the blood by metabolomic network analysis. Because metabolism is the final fingerprint of functionality and has been implicated in neurodegeneration, metabolomic network analysis can be used for refining the relationships between specific gene expression and metabolites and axonal damage in progressive MS. Ultimately, we hope to develop blood, CSF and stool-based assays, and use this comprehensive profile to predict susceptibility and progression of MS. This is a new and innovative idea, which will hope to lead to future diagnostic and therapeutic development in MS.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Stable clones of Control lentiviral (CLV) or lentiviral Noxa knockdown cells (NshLV7) (as described in Lowman et al, 2010) were counted at T-18hr and 60E6 cells were resuspended in 100ml of fresh complete medium. At T0 cells were counted again and 20E6 were collected into triplicate tubes. Cells were washed 1X with ice cold PBS and resuspended in 300ul ice cold methanol. Cells were then snap frozen in liquid nitrogen and stored at -80C. An additional 10E6 cells were collected for protein concentration and Western blot analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human oral keratinocytes growth and proliferation based on culture medium volume
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We seeded cells at density of 500k/T75 and cultured them at two different medium volume, one at 30ml, the other at 15ml. Culture medium is composed of 1x EDGS and 0.06mM calcium. We changed medium every day for 30ml culture, and every two days for 15ml culture. We collected spent medium when we changed medium. The collected spent medium was filtered through low protein binding 0.22um pore size filter and then stored at -80 degree C. For OA and SMT, spent medium was collected on the same day of D5 and D9 after cell seeding as marked on the tubes. For GK samples, 15ml and 30ml cultures were collected when cells reached at around 90% confluence, that is D5 for 15ml and D6 for 30 ml culture. The numbers 151, 152 were duplicated cell cultures in two T75s, same for 301 and 302. One major differences among GK, OA, and SMT is GK was from frozen cells; OA and SMT were fresh cells that were never frozen. Blank15 and Blank30 were complete medium without cells incubating in incubator for two days for Blank15 and one day for Blank30. Medium was collected in the same manner as others.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolites produced by strains associated with inflammation
STUDY_TYPE
MS analysis
STUDY_SUMMARY
EXPERIMENT 1: identify commonalities and differences between species at late log phase. EXPERIMENT 2: identify commonalities and differences within a species in function of the media used for the subset of bacteria cultured in more than one media. EXPERIMENT 3: identify commonalities and differences within a species in function of the growth phase for the subset of strains for which more than one time point was taken during the growth phase. Factor 1: growth phase for this slow growers as defined by early, mid and late log phase. Factor 2:rich media used for growth which are either NOS or OMIZ supplemented or not of TPP (thiamine pyrophosphate) a required supplement for some strains. Factor 3: cell pellet and supernatant of culture in which bacetria excrete small molecules. Factor 4. the bacterial species. All those bacteria come from the same genus and have been isolated in function of inflmmatory conditions in human.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Lanthanide-mineral induced alteration of bile acid metabolism in a murine model of steatohepatitis
STUDY_TYPE
MS analysis
STUDY_SUMMARY
120 mice (equal number of males and females) were randomized into 3 equal groups. One group is on a high-fat Western-style diet (HFWD) alone, a second group is on HFWD supplemented with lanthanides and calcium, and a third control group is supplemented with calcium alone. At study termination (18 months) we will harvest hepatocytes and colonic enterocytes for evaluation of epithelial gene expression patterns. We will also harvest cecal contents and feces for microbial profiling by 16S rRNA pyrosequencing. For this small pilot proposal, we wish to add an untargeted metabolomic analysis component. We will harvest liver (right medial lobe with gall bladder), serum, and feces. We will assay representative liver/gall bladder samples (8 from the HFWD group and 8 from the lanthanide/calcium supplemented group). Remaining liver samples and the serum and feces will be archived for future investigation. Liver is being targeted first since both steatohepatitis and hepatocellular carcinoma were seen in our previous study in mice on HFWD. Additionally, alterations of bile acid profiles and bile acid metabolism have been associated with both steatohepatitis and hepatic cancers.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Differences in bile acids composition between ASCL5 knockout and floxed mice.
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Understand the differences in Bile Acid composition between knockout and floxed mice at each intestinal segment. Also difference in metabolites between these two groups at each level of the intestine.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Pilot metabolomics study of aromatase inhibitor associated arthralgias
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The goal of the experiment is untargeted metabolomic and shotgun lipidomic profiling of serum samples collected from 50 patients before patients initiated therapy with an aromatase inhibitor and again after 3 months of aromatase inhibitor therapy. Half of the patients discontinued treatment within 6 months because of development of arthralgias during therapy and half remained on therapy for at least 24 months without development of significant arthralgias. We plan to analyse effects of AI therapy on metabolomic and lipidomic profiles, and to investigate associations between changes in profiles and development of symptoms.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Brain-Immune system-Gut Interaction in Chronic Mild Stress (CMS +/- Lacto)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Mice were devided into three groups (Naive untreated, Stressed untreated, Stressed + Lacto). The stressed groups were subjected to unpredictable chronic mild stress for seven weeks. Three weeks into the protocol, the +Lacto groups were administered probiotic Lactobacillus daily.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Cytokines correlation with metabolomic profiling of psoriatic and normal skin
STUDY_TYPE
MS analysis
STUDY_SUMMARY
These experiments are cytokine stimulations (TNF, IL-17, IFNg) of three keratinocyte lines (HAHA, PAK and BS4). Aim is to determine the metabolic changes induced by these cytokines and correlate with metabolomic profiling of psoriatic, uninvolved and normal skin.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human vitreous was collected in the OR at time of indicated surgery. No treatments were involved. Diagnoses are: epiretinal membranes (ERM); proliferative diabetic retinopathy (PDR); retinal detachment (RD)
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Differences in metabolism in mouse embryonic fibroblasts (control vs SCF-beta-TrCP knockout)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Mouse embryonic fibroblasts were grown in DMED supplemented with 10%FBS. The same number of cells were plated in eight 6cm dishes. When the cells were ~70% confluent, four dishes received ethanol (carrier) and the other four received tamoxifen (1uM final) to induce knockout. The cells and media were harvested 4 days later. The media harvested from control and knockout dishes will be compared with the starting medium. The cells were washed with cold PBS twice while they are attached to the dishes. The whole dish with cells attached were immediately frozen in dry ice and wrapped with aluminum foil and stored at -80C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
NIH 3T3 fibroblast cells with Ceftriaxone Treatment
STUDY_TYPE
MS analysis
STUDY_SUMMARY
NIH 3T3 cells were plated at 1.5million cells per 10cM dish into 12 10cm dishes. 24hrs post plating media was changed on all plates. At the time of media change, 4 dishes were treated with a final concentration of 50uM ceftriaxone (24hrs ceftriaxone n=4). 23 hrs post media change, 4 separate dishes were treated with 50uM ceftriaxone for 1hr (1hr ceftriaxone n=4). 4 dishes were untreated (0hr, basal, n=4). 24 hrs post media change, media was quickly removed from all 12 plates, each plate was rapidly washed with MilliQ H2O and rapidly frozen with liquid nitrogen poured directly into the dishes. All plates were transferred to dry ice and stored at -80 until shipped.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Short chain Fatty Acid (SCFA) analysis in HIV patients
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We hypothesize that a microbiome enriched with anaerobes in HIV leads to SCFA production and immunomodulatory effects. The goal of the experiment is evaluating bacterial metabolic pathways leading to production of SCFA. DLCO stands for Diffusing capacity of the lungs for carbon monoxide.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The effect of acetate on intestinal microorganisms
STUDY_TYPE
MS analysis
STUDY_SUMMARY
8 week old B6 Male: HFD+ Glucose, 9 day feeding; Blood collection from tail every 3 days; mice were fed glycerol (control) or GTA with increasing concentrations; Day 1-3 0.1g/kg; Day 3-6 1g/kg; Day 6-9 6g/kg
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Plasma from young adult mice, fasted 4 hr prior to bleeding. Key comparisons: Snell dwarf vs Snell normal. GHRKO KO vs WT. PAPPA KO vs Het. And two factor ANOVA: LivGHR KO, LivGHR WT vs GHRKO and GHRWT. Consistency between Snell, GHRKO, and PAPPA will be a major theme in the analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effect of DASH Diet on Gut Microbiome (SCFA from stool)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
This research will examine the effect of the currently recommended DASH diet versus a Vegetarian DASH diet on the gut microbiome and risk for cardiovascular disease in pre-hypertensive obese African American women. We will define the gut microbiota profile, short chain fatty acid production, breath hydrogen/methane response, plasma lipopolysaccharide production and other biomarkers of inflammation in response to diet type in obese African American pre-hypertensive females at baseline and following placement on the traditional DASH plan or DASH Vegetarian diet. We will also define these parameters in African American women adhering to a Vegetarian or Vegan Diet. Our goal is to determine how the gut microbiome modulates host physiology and immune function in response to diet type. By evaluating the effect of a recommended DASH dietary pattern versus a Vegetarian DASH plan on the gut microbiome and its fermentation products, we aim to identify novel information about how these diet types strategically reduce cardiovascular disease risk through gut:microbiota:host interaction.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
5
TOTAL_SUBJECTS
13
STUDY_COMMENTS
We will define the gut microbiota profile, short chain fatty acid production, breath hydrogen/methane response, plasma lipopolysaccharide production and other biomarkers of inflammation in response to diet type in obese African American pre-hypertensive females at baseline and following placement on the traditional DASH plan or DASH Vegetarian diet. We will also define these parameters in African American women adhering to a Vegetarian or Vegan Diet. Our goal is to determine how the gut microbiome modulates host physiology and immune function in response to diet type. By evaluating the effect of a recommended DASH dietary pattern versus a Vegetarian DASH plan on the gut microbiome and its fermentation products, we aim to identify novel information about how these diet types strategically reduce cardiovascular disease risk through gut:microbiota:host interaction.
Hamsters were treated with Clindamycin, or a Saline, or nothing at all. After four days animals were sacrificed and their cecal contents were collected to record change in their Microbiome. Along with the Microbiome analysis we are also performing metabolomics analysis to understand the influence of change in the microbiome with the metabolic changes (if any). The cecal contents collected were frozen immediately (using liquid nitrogen) and was frozen in -80C until analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic effects of weight reduction of very low energy diet vs dietary counseling
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The goal of the study is to assess the relative efficacy of a very low energy diet (VLED) using liquid meal replacement vs. standard of care dietary counseling and education (DCE) on the metabolic effects of weight reduction in the obese, subfertile population and assess ovulation and time to conception in these women. Subfertile women were recruited for this study. They completed an OGTT at baseline and again after completing a very low energy diet intervention.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Microbial ecology of nontuberculous mycobacteria (NTM) in cystic fibrosis (CF) sputum
STUDY_TYPE
MS analysis
STUDY_SUMMARY
These are sputum samples collected from 8 individuals with cystic fibrosis during the course of routine clinical care. They were initially stored at 4C for up to 24 hours then stored at -80C. No processing has been done to the sputum prior to freezing. For each individual there are sputum samples collected both before and after the individual had his or her first positive sputum culture for nontuberculous mycobacteria (NTM). The individuals experienced different clinical courses after their infection.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Diabetic heart adrenergic signaling and metabolism (STZ & Isoproterenol, High Fat)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We are examing the effect of both diabetes and adrenergic activation on the metabolomic profile. STZ treatment was initiated 5 months before hearts were harvested. High fat/low fat diets were given for 13 weeks. All hearts were excised in the morning. For the STZ/isoproterenol experiment, mouse anesthesia was initiated with 4% isoflurane, and maintained with 2% and a homeothermic controller. After 5 min of equilibration, control and fasted mice were injected intraperitoneally with either saline (S) or 25ug/kg isoproterenol (I). After an additional 5 min, the whole heart was quickly excised, washed with ice-cold distilled water, dried off with a chem whipe, and flash frozen in liquid nitrogen. Hearts were stored at -80, and shipped using dry ice. The hearts from the high fat diet experiement were prepared in the same way, but no injection was given and total anesthesia time was 5min instead of 10min.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic profiling of cyst fluid from patients with Intraductal Pancreatic Mucinous Neoplasm
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The pancreatic cyst fluids were collected using a syringe aspiration of the cyst fluid immediately after surgical resection of the lesion. The cyst fluid were then aliquoted and stored in -80C freezer until ready to use. We plan on performing untargeted metabolomics analysis on these pancreatic cyst fluid to find potential biomarkers that correlate with histopathological assessment and clinical behavior of these cystic lesions and thus to guide clinical management of patients.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effect of genetic lesions on glioblastoma (NP, NPA, NPAI, NS)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The cells in this experiment are primary cells derived from tumors with various genetic lesions. The purpose of this experiment is to determine the effect of the genetic lesion IDH1m (mutant isocitrate dehydrogenase) on the metabolic state of the cell. Four replicates of NPA versus four replicates of NPAI suspension cell neurospheres will be compared in an untargeted manner to identify all possible metabolic differences between the two types of genetic lesions.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of lean males given water, antibiotic cocktail (ANMV), or neomycin then exposed to ozone
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Mice were given either water, an antibiotic cocktail (ANMV), or Neomycin in their drinking water for two weeks to reduce bacterial load, and then exposed to air or to ozone (2ppm for 3hrs). 24 hours later, pulmonary mechanics and airway responsiveness was assessed, and blood was collected via cardiac puncture. Serum was isolated and immediately stored at -80 C for further analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomic Profiles of Recovery from Traumatic Brain Injury
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We hypothesize that differences between the metabolome of TBI patients achieving full recovery at 3 months post-injury and those with protracted recovery will provide insights into the biology of recovery and yield novel biomarkers for predicting protracted recovery. To test our hypothesis, we will perform a case-control study examining the metabolomic profile of 128 TBI patients, 18 years and older, who either have complete functional recovery at 3 months post-injury or have functional decline at 3 months post-injury. Subjects were selected from an ongoing prospective cohort of traumatic brain injury (Head Injury Serum Markers for Assessing Response to Trauma, HeadSMART. Funding for HeadSMART was provided by ImmunArray.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Replicate populations of Aedes albopictus were reared under diapause-inducing short day photoperiod (8h light: 16h dark) and diapause-averting long day photoperiod (16h light:8h dark). Eggs were collected from each replicate and snap-frozen 11d post-oviposition. We hope to characterize the metabolomic and lipidomic profiles of diapausing eggs relative to non-diapause eggs.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Analysis of SCFA in the fecal matter of wt and Orai1kO mice
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The gut microbiome participates in numerous physiological functions and is believed to be shaped by the host intestine. We report here an unsuspected prominent role of Orai1-mediated pancreatic acinar cell exocytosis in shaping the microbiome. Deletion of Orai1 in pancreatic acini of mature mice maintained on solid diet resulted in 60-70% mortality. The mice have severe bacterial burden with dysbiosis resulting in systemic inflammation and death. This occurs despite prominent Paneth cell hyperplasia and activation of the intestinal innate immune response. Secretion of and bacterial killing by pancreatic defensins are markedly reduced, resulting in microbiota with decreased diversity and increased pathogenic bacteria. Survival and weight gain are not rescued by digestive enzyme supplements, but are by broad-spectrum antibiotics and purified liquid diet. These findings reveal an unexpected profound role of pancreatic secretion in shaping the microbiome
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics has recently been used to document age-related changes in key metabolic pathways in laboratory animals and as a biomarker to predict age. We study the ecology, evolution, behavior, and physiology of wild North American red squirrels where we are able to follow individual squirrels across their lifetime from birth until death. We are beginning to document aging in this natural population and are interested in understanding whether there is a signature of aging using metabolomics. We collected plasma samples from the oldest female and male squirrels in our study population and also from an equivalent number of younger squirrels. We will use an untargeted approach to provide an assessment of what metabolites differ among very old and young squirrels. The aim of these analyses is to allow us to identify if the same metabolites that have been identified as biomarkers of advanced age from laboratory mice are also biomarkers of advanced age in red squirrels. After we complete these untargeted analyses, we aim to develop a metabolomics panel for this species so that we can use a more targeted approach to assess how the metabolic profiles of specific pathways (glucose/fatty acid metabolism, redox homeostasis) change with age in offspring exposed to increased perinatal stress in our study species.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
6
TOTAL_SUBJECTS
33
STUDY_COMMENTS
Metabolomics has recently been used to document age-related changes in key metabolic pathways in laboratory animals and as a biomarker to predict age. We study the ecology, evolution, behavior, and physiology of wild North American red squirrels where we are able to follow individual squirrels across their lifetime from birth until death. We are beginning to document aging in this natural population and are interested in understanding whether there is a signature of aging using metabolomics.
Metabolome, body composition, and muscle performance in children
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The purpose of this study is to determine potential relationships between plasma metabolome patterns and body composition in addition to muscle quality and muscular performance in children. Children ages 8 to 10 will complete body composition testing including BMI and skin fold measurements. An ultrasound machine will be used to determine cross-sectional area and echo intensity in the vastus lateralis and rectus femoris muscles as a measure of muscle quality. Isokinetic leg extension strength, power, and fatigability will be determined from a series of maximal knee extensions using an isokinetic dynamometer. An untargeted metabolomics test will be used on a single plasma sample from each subject in order to examine plasma metabolome
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We intend to analyze 89 samples for Untargeted Metabolomics on patients with and without Polycystic Ovarian Syndrome(PCOS). Blood is drawn from patients at four different time points; 1st) 0 Timepoint at clamp 2nd) 270 Timepoint at clamp 3rd) 0 Timepoint at OGTT and 4th) 120 Timepoint at OGTT (a couple of samples were missing 120, but we included a 30 min sample and a 90 min sample and for some subjects OGTT samples are not included but not listed here). All samples are drawn in EDTA tubes at the Children's Hospital of Colorado. Collected blood is processed and frozen immediately at -80 degrees celcius.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
This is a double blind study, to measure short chain fatty acids in colons of mouse that have gone through bariatric surgery and the mouse that have gone through sham surgery (as control group). We would like to get a ratio of different types of fatty acids in the colons of these animals. This project looks at the effects of bariatric surgery on short chain fatty acids produced by microbiota ultimately the effects on the growth and suppression of breast cancer.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effects of bariatric and antibiotic treatment surgery on mammary carcinogenesis
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The purpose of this study is to understand the effects of bariatric surgery on mammary carcinogenesis in C3 Tag (1) mouse model. My animals have gone through antibiotic treatments in drinking water vs. no abx in their water. Also animals have been though vertical sleeve gasteroctomy (VSG) vs sham surgery vs no surgery group. It is expected that these surgeries will affect the tumor proliferation and growth. One potential explanation can be the changes of SCFAs following the bariatric surgery.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of rats after bariatric or sham surgery
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We would like to examine the levels of amino acids in rats who have underwent bariatric (VSG, vertical sleeve gastrectomy) or sham (control) surgery. Plasma was collected after an overnight fast and once again after refeeding the rats for 2 hours.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The aim of this study is to determine whether changes in CoA degradation affect the composition of the acylcarntine pool in the liver. 7 wild-type and 7 Nudt7 knockout male mice (10-16 weeks of age) on a mixed background were fasted for 24h and allowed to refeed for 12-14hours before removing the liver. The liver samples were flash-frozen and stored at -80C until used.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Microbial changes following fecal microbiota transplantation in patients with recurrent C. difficile infection
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Fecal samples were collected from patients with recurrent Clostridium difficile infection before and after treatment with fecal microbiota transplantation. Fecal samples were frozen immediately after collections, and later put into ~50mg aliquots for later analysis (at -80 C).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Measuring SCFA in mice gut following colonization by C. difficile
STUDY_TYPE
MS analysis
STUDY_SUMMARY
3 cages of 5-8 week old C57B/6 mice were placed on the antibiotic cefoperazone for 10 days followed by 2 days of reovery on plain water. One cage remained on plain water the entire time. Of the three antibiotic treated cages. One was mock infected (uninfected control), one was infected with C. difficile strain VPI 10463, while the other was infected with C. difficile strain 630. Twenty-four hours after the infection the mice were eutanized and the ceal content was collected and snap frozen in liquid nitrogen. Samples were stored in the -80 until analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Murine bile acid profiles during CDI R20291 infection
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We are interested in understanding the bile acid profiles in cecal content from mice challeneged with R20291 C. difficle spores. We are also interested in the bile acid profiles of mice that are administered Ursodiol (UDCA) or vehcile (corn oil) during C. difficile infection. In vitro Ursodiol (UDCA) has significant impacts on germination and growth of C. difficile R20291.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic change in macrophages after efferocytosis
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Study metabolic pathway alteration in macrophages after efferocytosis (when macrophages eating apoptotic cells). Peritoneal macrophages were purified and plated in the cell-culture dishes. After culturing overnight. Apoptotic cells were overlayed to macrophages for 2 hours, then un-engulfed cells were removed through washing. Macrophages were left in the plate for another 4 hours before being lifted from the plate.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic change in macrophages after efferocytosis (part II)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The goal of the experiment is to study metabolic pathway alteration in macrophages after efferocytosis (when macrophages eating apoptotic cells). Peritoneal macrophages were purified and plated in the cell-culture dishes. After culturing overnight. Apoptotic cells were overlayed to macrophages for 2 hours, then un-engulfed cells were removed through washing. Macrophages were left in the plate for another 4 hours before being lifted from the plate.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolite-phenotype link in X-linked Adrenoleukodystrophy (fibroblast cell culture)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Untargeted metabolomics of control, AMN and ALD patient-derived fibroblasts. Fibroblasts cultured in DMEM with 15%FBS and antibiotic (pen/strep) in 100mm petridishes (1million/dish). After 24h cultures supplemented with fresh media (DMEM+15%FBS+antibiotic) for 3hr
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolite-phenotype link in X-linked Adrenoleukodystrophy (part II)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Untargeted metabolomics of control, AMN and ALD patient-derived fibroblasts. Human Postmortem brain tissue were obtained from NICHD Brain Bank. Brain regions were directed by the neuropathologist at Henry Ford Health System and sample tissue were immediately frozen at -80C until shipping to the UMICH Core.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human patients were enrolled in a bariatric weight loss clinic and followed. Patients were male and female, normoglycemic,pre-diabetic and diabetic and with and without neuropathy. One 500 ul aliquot will be submitted for both untargeted metabolomics and shotgun lipidomics.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of intensive weight management clinic (IWMC) weight loss
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Human patients were enrolled in a weight loss clinic and followed. Patients were male and female, normoglycemic,pre-diabetic and diabetic and with and without neuropathy.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of mice inoculated with human microbiota
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Mice were inoculated with human microbiota. Peripheral blood was collected using superficial temporal phlebotomy into a tube containing EDTA-K2. Tubes were then inverted 5 times and placed on ice for no longer than one hour. Samples were centrifuged at 1500rcf for 15 minutes. Supernatant was transferred and quantified with a pipette. Tubes were placed on dry ice for between 10 minutes to an hour andl stored at -80C until shipped on dry ice. All steps during processing were performed in batches containing mulitple treatment groups.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Blood was collected from the facial vein of humanized mice immediately prior to euthansia via CO2 inhalation. Blood sat at room temperature for 20 minutes, and then was centrifuged at 12000g for 10 minutes at 4 C. Serum was removed to a new eppendorf tube and immediately placed on ice, and then samples were subsequently stored at - 20 C until the present.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of mice inoculated with human stool (part III).
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Mice were inoculated with human stool samples from donors in a high gene copy number group or low gene copy number group. After several weeks, cecal contents were collected and frozen at -80. Aliquots were made on dry ice and then stored at -80 until shipment on dry ice. Analysis of short chain fatty acids (SCFA) of cecal content was performed.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
BeWo cells were plated in 100mm x 20mm cell culture plates and allowed to attach and acclimate for 24 hours. Cell culture media was then replaced with media containing mono(2-ethylhexyl)phthalate (MEHP) at either 90 or 180 micromolar concentrations or vehicle control (DMSO, 0.05% by volume). Cells were exposed for 24 hours followed by collection of cell media which was flash frozen in liquid nitrogen and then placed on dry ice. Cells were washed with sodium acetate and then immediately flash frozen by addition of ~8mL of liquid nitrogen to tissue culture plate. All samples were stored at -80 degrees C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Pregnant rats were treated for 5 days with 100mg/kg/day DEHP or vehicle control (corn oil) via a wafer which the rats consumed orally. After the fifth treatment, rats were euthanized and uterine horns were dissected. Amniotic fluid was collected from the gestational sac via syringe and collected into 1.5mL tubes. Tubes were then stored at -80 celsius
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Pregnant rats were treated for 5 days with 100mg/kg/day DEHP or vehicle control (corn oil) via a wafer which the rats consumed orally. After the fifth treatment, rats were euthanized and uterine horns were dissected. Amniotic fluid was collected from the gestational sac via syringe and collected into 1.5mL tubes. Tubes were then stored at -80 celsius.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Pregnant mice were treated for 14 days (from GD 0.5-13.5) with 125mg/kg/day DEHP or vehicle control (corn oil) via oral gavage. After the last treatment, mice were euthanized and placenta were removed and flash frozen in liquid nitrogen. Placentas were then stored at -80 celsius.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Thermal modalities are commonly used in sports medicine to affect tissue healing. Cold therapy is commonly used modalities, but the metabolic changes to muscle after cooling are not known. The objective of this study is to look at the effect of cooling on muscle metabolites and gene expression. There are a total of 8 subjects in the study. Each subject had an ice cup cryotherapy treatment (cool samples) to one leg for 15 minutes, and the other leg served as the control (cntrl samples). Two hours after the application of cryotherapy, a biopsy was taken from each thigh muscle. Muscle was minced with scissors and quickly snap frozen in liquid nitrogen.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
10
TOTAL_SUBJECTS
8
STUDY_COMMENTS
We would like to run the TCA Plus Analysis on each of the samples. For the statistical analysis, we would normalize the cool side to the ctrl side, and look at the relative change in metabolite abundance as a result of the cooling procedure. only used in sports medicine to affect tissue healing.
Comparison of the metabolome and lipidome of wild type and mdx/mTR mice
STUDY_TYPE
MS analysis
STUDY_SUMMARY
There are two groups of mice in the study, wild type mice (WT) and mdx/mTR mice (mdx or mdx/mTR) that are a model of musclar dystrophy. We collected the tibialis anterior muscles from these mice (N=6 in each group), and would like to perform TCA-plus analysis and shotgun lipidomics analysis on the mice, and compare across the two groups.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Rat Retinal Detachment Metabolomics Timecourse (part II)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Detachments were created in adult male Brown-Norway rats (300?400 g; Charles River Laboratories, Wilmington, MA). Briefly, rodents were anesthetized with a 50:50 mix of ketamine/xylazine, and pupils were dilated with topical phenylephrine (2.5%) and tropicamide (1%). A 20-gauge microvitreoretinal blade was used to create a sclerotomy 2 mm posterior to the limbus, carefully avoiding lens damage. A subretinal injector (Glaser, 32-gauge tip; BD Ophthalmic Systems, Franklin Lakes, NJ) was introduced through the sclerotomy into the vitreous cavity and then through a peripheral retinotomy into the subretinal space. Sodium hyaluronate (10 mg/mL, Healon OVD; Abbott Medical Optics, Uppsala, Sweden) was slowly injected to detach the neurosensory retina from the underlying RPE. In all experiments, approximately one third to one half of the neurosensory retina was detached. Detachments were created in the left eye. The right eye served as the control, with all the steps of the procedure performed except for introduction of the subretinal injector and injection of the sodium hyaluronate. At varying intervals after creation of the detachment, the animals were euthanatized, and the eyes were enucleated.The retina was then dissected away from the retinal pigment epithelium taking just the detached portion in those eyes experimentally detached. All experiments were performed in accordance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research and the guidelines established by the University Committee on Use and Care of Animals of the University of Michigan. Detachments were created in adult male Brown-Norway rats (300?400 g; Charles River Laboratories, Wilmington, MA).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
10
TOTAL_SUBJECTS
27
STUDY_COMMENTS
All experiments were performed in accordance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research and the guidelines established by the University Committee on Use and Care of Animals of the University of Michigan. Detachments were created in adult male Brown-Norway rats (300?400 g; Charles River Laboratories, Wilmington, MA).
Metabolomics of cilia and modulation of renal microcirculation
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Explore and explain the mechanism of regulation of metabolism biomarkers to modulate renal microcirculation. 1 - let rats rest for 5 days. 2 - test basal glucose and plasma. Store plasma in -20C for one day then transfer to -80. 3 - inject STZ 50mg/kg ip. 4 - after 3 days, check for increased glucose and extract plasma for early stage diabetic sample >300 mg/dl. Store in -20C and then -80C. 5 - one month after initial injection, extract plasma and store in -20C and then -80C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Tubuloglomerular feedback and salt-sensitive hypertension
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Collect whole blood in tubes containing EDTA, gently invert tubes 10 times and cool as soon as practical on ice. Centrifuge to separate plasma as soon as practical, transfer to appropriately labeled tubes, and freeze immediately. I test basal glucose and plasma store plasma in -20C for one day then transfer to -80C. The next day, inject STZ 60 mg/kg ip. After 3 days, check for increased glucose and extract plasma for early stage diabetic sample >300 mg/dl. Store in -20C and then -80C. 30 days after initial injection, extract plasma and store in -20C and then -80C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
One year caloric restriction (CR) compared to ad lib (AL) feeding on metabolic and clinical parameters to assess association with intrinsic oxidative capacity. High and low capacity running rats (HCR and LCR) were randomized to ad lib feeding vs. 40% caloric restriction starting at 8 weeks of age. Experiment was continued for 52 weeks when blood and tissue were collected. Exercise capacity, CLAMS assessment of fuel utilization and clinical parameters were determined at 8 weeks, 8 months and 12 months of age. Tissue was collected in the fed (2 hours after re-feeding) or fasted stated all groups.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
N/NIH rats were selected for either low (LRT) or high (HRT) response to training. Rats at 2 year of age were trained for 8 weeks with an improvement in oxidative capacity. Selection was also performed for high (HCR) or low (LCR) intrinsic running capacity. Young and old animals are compared to 12 week old animals.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Plasma Nucleotide/adenosine concentrations in patiens with scleroderma depending on exercise
STUDY_TYPE
MS analysis
STUDY_SUMMARY
This experiment was performed using the following cohorts: 1) healthy controls, 2) patients with scleroderma at low risk for pulmonary hypertension, 3) pateints with scleroderma at high risk for pulmonary hypertension (SSc Cath). Whole blood was drawn directly into stop soilution (1:1 ratio) at rest and again at peak exercise for each human subject. The samples were processed to plasma by MCRU and stored at -80 in the Biorepository.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Untargeted metabolomics and lipidomics of scleroderma PAH discovery cohort
STUDY_TYPE
MS analysis
STUDY_SUMMARY
This experiment was performed using the following cohorts: 1) healthy controls, 2) patients with scleroderma at low risk for pulmonary hypertension, 3) pateints with scleroderma at high risk for pulmonary hypertension who underwent a catheterization and were found to have normal pressures, borderline elevated pressures or pulmonary arterial hypertensino (PAH). Whole blood was drawn directly into EDTA tubes at rest and again at peak exercise for each human subject. The samples were processed to plasma by MCRU and stored at -80 in the Biorepository.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Differences in metabolite profiles and antioxidant activities between wild and cultivated black soybeans evaluated by a correlation analysis
STUDY_SUMMARY
Non-targeted metabolic profiling of 26 soybean varieties using liquid chromatography-mass spectrometry (LC-MS) including 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), combined with multivariate analysis, revealed significant differences in 25 differential metabolites
INSTITUTE
KIST
LAST_NAME
Xu
FIRST_NAME
Jiuliang
ADDRESS
saimdang-ro 679, Gangneung, Gangwon, 213510, Korea, South
Metabolite analysis of regional neural stem/progenitor cells
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The developing mammalian brain generates a variety of Neural Progenitor Cells (NPCs). Primary NPCs throughout the neuraxis are derived from the ventricular zone. Intermediate progenitor cells (IPCs) are produced uniquely in the telencephalon and contribute extensively to the neurons that comprise the cerebral cortex and basal ganglia. It is known that the fate of the diverse NPC populations is determined by the interplay of transcription factors and regulation by regional humoral cues. However, despite our recent appreciation that nutrient-regulated intracellular metabolic milieu (pO2, energy, and redox state) significantly influence cell fate, an unexplored area is whether NPCs have intrinsic metabolic identity, and if so, the mechanism by which molecular metabolism contributes to brain development.Little is known however, if intrinsic differences in cellular metabolism of regional NPCs make certain NPCs susceptible while others resistant to genetic and environmental insults. We conjectured that regional (fore-and hindbrain) NPCs are metabolically distinct.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolites of human neurons and stem cells (siNeuron metabolomics)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
There are a total of four samples each for this analysis. Each sample consists of the cells grown on three 10 cm culture plates. Each plate should have 2x106 cells for a total of 6x106 cells per sample when all three plates are combined. The first sample is undifferentiated human embryonic stem cells, the second sample is human glutamatergic neurons derived from those human embryonic stem cells, the third sample is undifferentiated human induced pluripotent stem cells and the fourth sample is human glutamatergic neurons derived from those human induced pluripotent stem cells.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
From Lawson et al., Obesity 2015 (PMID: 25865294). Methods: A randomized, placebo-controlled crossover study of single-dose intranasal oxytocin (24 IU) in 25 fasting healthy men was performed. After oxytocin/placebo, subjects selected breakfast from a menu and were given double portions. Caloric content of food consumed was measured. Visual analog scales were used to assess appetite, and blood was drawn for appetite-regulating hormones, insulin, and glucose before and after oxytocin/placebo. Indirect calorimetry assessed resting energy expenditure (REE) and substrate utilization. Here, T0 refers to immediately before OXT or Placebo was administered (fasting), and T55 refers to 55 minutes post-administration (fasting, immediately pre-meal).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Looking for changes in lipid levels with knock out of ACADM (shACADM)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
GSC 8-11 cells (20 million) were transduced with lentivirus coding for shACADM 4, 6, or scr (control). ACADM is an enzyme responsible for the metabolism of medium chain fatty acids (C4-C12). A round of selection was performed using puromycin to ensure only cells that had been transduced survived. Knockdown of ACADM was confirmed via western blot. Pellets were collected by centrifuging cells for 10 min at max speed. The pellets were washed and each sample was split into quadruplicate.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic effects of novel aldehyde dehydrogenase inhibitors (ALDH) inhibitors
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Effect of novel aldehyde dehydrogenase inhibitors. Before an experiment medium was replaced to medium without glucose with addition of labeled glucose on C13. Next, cells were treated with ALDH inhibitors 673 or 773 for 1, 4, or 8 hr (673&773-Jan26)
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Michigan Biomarkers for Refractory Depression (Bluebird) metabolomics pilot study
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The goal of the project is discovery of clinical useful biomarkers for treatment-resistant depression. All participants were undergoing electroconvulsive therapy (ECT) for treatment-resistant depression (major depressive disorder or bipolar disorder) in 2012-2014. All subjects were Caucasian except BB060, who was Asian. Samples were collected from each subject at baseline just before the first ECT treatment (Time Point T0) and approximately 3 weeks later just before the tenth ECT treatment (Time Point T2). Whole blood was drawn in the morning in a fasted state (at least 7 hours) through an intravenous catheter or butterfly needle into 6-mL EDTA tubes (Lavender Top, Becton Dickinson Vacutainer K2EDTA additive blood collection tube, part #367863) and transported to the processing lab at the Michigan Clinical Research Unit within 30 minutes. Plasma was isolated by centrifugation for 10 minutes at 2000G at 4C. Plasma from multiple tubes was pooled and aliquotted in 200 uL volumes into 2-mL screw-cap cryovials and frozen at -80C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic Adaptations to Chronic and Acute Exercise in Overweight Adults (ATX-Study) preliminary data
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The primary purpose of this study is to examine the effects of chronic exercise training and an acute session of exercise on key risk factors associated with Metabolic Syndrome (e.g., glucose tolerance, blood lipid profile, and blood pressure) and alterations in subcutaneous adipose tissue structure and metabolic function in overweight adults. Human adipose tissue samples collected before, and one hour after a 1h exercise session at ~65% VO2max (maximal oxygen uptake)
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Lipidomics pilot project for mice exposure to bisphenol A and high fat diets
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Wild type (a/a) agouti mouse dams were randomized to one of three diets (control, Mediterranean, western) two weeks prior to pairing with an agouti (Avy/a) sire. Diet exposure continued through pregnancy and lactation. All pups were weaned onto the control diet and then followed for metabolic phenotyping measures to 10 months of age. Comprehensive phenotyping (body composition, CLAMS, blood draw) was completed at 2, 4, and 8 months, with an OGTT at 8 months. Weekly weights were also recorded. The study examines whether prenatal dietary exposure to high fat diets (HFD) and bisphenol a (BPA, those groups will not be tested in this pilot) impacts metabolic programming in offspring as measured by hepatic steatosis, serum hormone levels, and epigenetic changes in hepatic lipid metabolism genes. Shotgun lipidomics will add insight into the potentially changing lipid composition of membranes in offspring following different prenatal diet exposures as a means of assessing risk of steatosis and metabolic changes.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Six strain/genotype combinations (BKS wt, BKS db/+, ?) were fed control (5LOD) or high fat (54 % lard) chow from 5 to 36 weeks of age. Longitudinal changes in small and large nerve fiber function, glucose tolerance, fasting blood glucose, body weight etc. were assessed in all groups
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Absolute Quantification of 180 metabolites in serum from african american and european american in prostate cancer and case control samples
STUDY_SUMMARY
Metabolite concentrations were obtained in prostate cancer and case control plasma samples from AA and EA individuals using the AbsoluteIDQ kit p180 (Biocrates Life Science AG, Austria) according to the manufacturer’s instructions. The analysis was performed using a QTRAP 6500 LC/MS/MS System (AB SCIEX, USA) equipped with an electrospray ionization source, Agilent G1367B autosampler and the Analyst 1.51 software (AB SCIEX, USA).
metabolome in a group of AA and EA matched pairs of prostate cancer (PCa) and benign adjacent tissues
STUDY_SUMMARY
10 µL of suspended samples was injected and analyzed using a 6495 triple quadrupole mass spectrometer (Agilent Technologies, Santa Clara, CA) coupled to a HPLC system (Agilent Technologies, Santa Clara, CA) via Multiple reaction monitoring (MRM) of a total of 240 endogenous water soluble metabolites for steady-state analyses of samples. Those 240 compounds monitored were chosen due to their involvement in central pathways important in a number of malignancies. Source parameters were as follows: Gas temperature was 250 °C; Gas flow was 14 l/min; Nebulizer was 20psi; Sheath gas temperature was 350 °C; Sheath gas flow was 12 l/min; Capillary was 3000 V positive and 3000 V negative; Nozzle voltage was 1500 V positive and 1500 V negative. Approximately 8–11 data points were acquired per detected metabolite. Samples were delivered to the MS via normal phase chromatography using either a 4.6 mm i.d ×10 cm Amide XBridge HILIC column (Waters) or a Luna 3µ NH2 100A (Phenomenex) at 300 µL/min
An untargeted metabolomics approach was utilized to determine urinary metabolites that could serve as small molecule biomarkers for treatment response to standard tuberculosis treatment. However, the majority of metabolites that most accurately distinguished patient samples at time of diagnosis from those at one month after the start of therapy lacked structural identification. The detection of unknown metabolite structures is a well-known limitation of untargeted metabolomics, and underscores a need for continued elucidation of novel metabolite structures. In this study, we sought to define the structure of a urine metabolite with an experimentally determined mass of 202.1326 Da, classified as molecular feature (MF) 202.1326. A hypothesized structure of N1-acetylisoputreanine was developed for MF 202.1326 using in silico tools and liquid chromatography-tandem mass spectrometry (LC-MS/MS). In the absence of a commercial standard, synthetic N1-acetylisoputreanine was generated using enzymatic and chemical synthesis and LC-MS/MS was used to confirm the structure of MF 202.1326 as N1-acetylisoputreanine, a proposed terminal polyamine catabolite that had not been previously detected in biological samples. Further analysis demonstrated that N1-acetylisoputreanine and an alternative form of this metabolite, N1-acetylisoputreanine-γ-lactam, are both present in human urine and are likely end-products of polyamine metabolism.
Identifying metabolic adaptations characteristic of multiple myeloma cells via mass spectrometry-based metabolite profiling from Peripheral Plasma
STUDY_SUMMARY
Will be assessing the untargeted metabolomic profiles of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma, bone marrow plasma and Cd138+ plasma cells. Peripheral Plasma ms5972
INSTITUTE
Mayo Clinic
LAST_NAME
Gonsalves
FIRST_NAME
Wilson
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Identifying metabolic adaptations characteristic of multiple myeloma cells via mass spectrometry-based metabolite profiling from Bone Marrow Plasma
STUDY_SUMMARY
Will be assessing the untargeted metabolomic profiles of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma, bone marrow plasma and Cd138+ plasma cells. Bone Marrow Plasma ms5973
INSTITUTE
Mayo Clinic
LAST_NAME
Gonsalves
FIRST_NAME
Wilson
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Identifying metabolic adaptations characteristic of multiple myeloma cells via mass spectrometry-based metabolite profiling from (CD138+ Plasma Cells)
STUDY_SUMMARY
Will be assessing the untargeted metabolomic profiles of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma, bone marrow plasma and Cd138+ plasma cells. Cd138+ plasma cells ms5974
INSTITUTE
Mayo Clinic
LAST_NAME
Gonsalves
FIRST_NAME
Wilson
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Identifying metabolic adaptations characteristic of multiple myeloma cells via targeted sphingolipids concentrations from bone marrow and peripheral plasma
STUDY_SUMMARY
Will be assessing the targeted sphingolipids concentrations of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma and bone marrow plasma.
INSTITUTE
Mayo Clinic
LAST_NAME
Gonsalves
FIRST_NAME
Wilson
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Identifying metabolic adaptations characteristic of multiple myeloma cells via amino acids concentrations from bone marrow plasma
STUDY_SUMMARY
Will be assessing the targeted amino acids concentrations of high risk versus low risk smoldering myeloma patients based on peripheral blood plasma and bone marrow plasma.
INSTITUTE
Mayo Clinic
LAST_NAME
Gonsalves
FIRST_NAME
Wilson
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Large Untargeted Profiling of Myelin to Enhance Recovery of Function after SCI
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeted FFA Composition of Myelin to Enhance Recovery of Function after SCI
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeted NEFA Panel of Myelin to Enhance Recovery of Function after SCI
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeted Cholesterol Profiling of Myelin to Enhance Recovery of Function after SCI
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeted Sphingolipids Panel of Myelin to Enhance Recovery of Function after SCI
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeted Galactosyl Sphingolipids Concentrations of Myelin to Enhance Recovery of Function after SCI
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeted Sphinomyelin Panel of Myelin to Enhance Recovery of Function after SCI
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeted TCA Panel of Myelin to Enhance Recovery of Function after SCI
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics
STUDY_TYPE
Observational
STUDY_SUMMARY
The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls. Through targeted and untargeted metabolomics analyses we confirm earlier reports of specific alterations in plasma levels of choline, carnitine and complex lipid metabolism in ME/CFS. We also demonstrate that patients with ME/CFS and IBS have a unique metabolomic profile that includes increased plasma levels of ceramide, a waxy lipid implicated in suppression of electron transport, insulin and leptin resistance and apoptosis. Integration of fecal metagenomic and plasma metabolomic data resulted in a stronger predictive model of ME/CFS (cross-validated AUC=0.836) than either metagenomic (cross-validated AUC=0.745) or metabolomic (cross-validated AUC=0.820) analysis alone. Our findings may provide insights into the pathogenesis of ME/CFS and ME/CFS subtypes, and suggest pathways for the development of diagnostic and therapeutic strategies.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
Key: mecfs : 1 in this column indicates case, while 0 indicates control Ibs: 1 in this column indicates the patient does have disease, 0 indicates free of ibs
Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics
STUDY_TYPE
Observational
STUDY_SUMMARY
The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
Key: mecfs : 1 in this column indicates case, while 0 indicates control Ibs: 1 in this column indicates the patient does have disease, 0 indicates free of ibs
Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics (part III))
STUDY_TYPE
Observational
STUDY_SUMMARY
The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls. Through targeted and untargeted metabolomics analyses we confirm earlier reports of specific alterations in plasma levels of choline, carnitine and complex lipid metabolism in ME/CFS. We also demonstrate that patients with ME/CFS and IBS have a unique metabolomic profile that includes increased plasma levels of ceramide, a waxy lipid implicated in suppression of electron transport, insulin and leptin resistance and apoptosis. Integration of fecal metagenomic and plasma metabolomic data resulted in a stronger predictive model of ME/CFS (cross-validated AUC=0.836) than either metagenomic (cross-validated AUC=0.745) or metabolomic (cross-validated AUC=0.820) analysis alone. Our findings may provide insights into the pathogenesis of ME/CFS and ME/CFS subtypes, and suggest pathways for the development of diagnostic and therapeutic strategies.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
Key: MECFS: 1 in this column indicates case, while 0 indicates control IBS: 1 in this column indicates the patient does have disease, 0 indicates free of IBS
Insights into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) phenotypes through comprehensive metabolomics (part IV)
STUDY_TYPE
Observational
STUDY_SUMMARY
The pathogenesis of ME/CFS, a disease characterized by unexplained debilitating fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, lymphadenopathy and irritable bowel syndrome (IBS), is poorly understood. There are no validated diagnostic tests or interventions to mitigate disease. Here we report association modeling, biomarker discovery, biochemical enrichment analysis and topological network visualization of plasma metabolomic, fecal bacterial metagenomic and clinical data from 50 ME/CFS patients and 50 healthy controls. Through targeted and untargeted metabolomics analyses we confirm earlier reports of specific alterations in plasma levels of choline, carnitine and complex lipid metabolism in ME/CFS. We also demonstrate that patients with ME/CFS and IBS have a unique metabolomic profile that includes increased plasma levels of ceramide, a waxy lipid implicated in suppression of electron transport, insulin and leptin resistance and apoptosis. Integration of fecal metagenomic and plasma metabolomic data resulted in a stronger predictive model of ME/CFS (cross-validated AUC=0.836) than either metagenomic (cross-validated AUC=0.745) or metabolomic (cross-validated AUC=0.820) analysis alone. Our findings may provide insights into the pathogenesis of ME/CFS and ME/CFS subtypes, and suggest pathways for the development of diagnostic and therapeutic strategies.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
Key: MECFS: 1 in this column indicates case, while 0 indicates control IBS: 1 in this column indicates the patient does have disease, 0 indicates free of IBS
The goal is to look at measures of overall metabolic state in relationship to hormonal environment and measures of mood/depression or cognitive function (behavioral and functional MRI images). There are some relationships in this data set between glucose/insulin levels and cognitive function, and we would like to use the untargeted assays to further investigate this relationship. Factors related to visual/spatial memory are included in the design. Factors 1 and 2 (Left Hippocampus, Right Hippocampus) are levels of activation in the hippocampus during a visual memory task, (data missing for some of the samples). Factors 3-5 (BVMT % Retained, BVMT Learning T, BVMT Delay T) are results from a cognitive test of spatial memory function.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The goal of this study was to characterize the metabolic impact manifested in mouse lung following acute ozone exposure, comparing differential effects experienced by lean and obese model mice.
Analysis of blood plasma lipid composition in patients with diabetic kidney disease In this untargeted lipidomics study we are comparing the lipidomics profile of progressors versus nonprogressors. A subgroup of patients have a follow up samples and therefore their baseline data are comared to the follow up visit data.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Dynamics of metabolism, proliferation and differentiation in Toxoplasma gondii mutants deficient in glycolysis and gluconeogenesis
STUDY_TYPE
Time course 13C labeling of Toxoplasma gondii using glucose and glutamine
STUDY_SUMMARY
The focus of this study was to profile the metabolic fates of glucose and glutamine in wild type, glycolytic mutant (hexokinase KO) and gluconeogenesis mutant (PEPCK1 KO) tachyzoite stage T. gondii parasites. 13C6-glucose and 13C5-15N1-glutamine were used as metabolic tracers. Metabolites from glycolysis, pentosephosphate pathway and Kerbs cycle were identified and their isotopomer abundance was quantified in order to visualize metabolic flux across the indicated pathways. A time course (from 0 minutes to 120 minutes) analysis was carried out in the labeling experiments. Here, host cell free extracellular tachyzoite stage T. gondii parasites were used.
INSTITUTE
CSIR-National Chemical Laboratory
DEPARTMENT
Biochemical Sciences Division
LABORATORY
Molecular Parasitology Laboratory
LAST_NAME
Shanmugam
FIRST_NAME
Dhanasekaran
ADDRESS
Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
Integrated nutrigenomic and metabolomic analysis of Africans with variable diet
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Untargeted metabolic profiling and lipidomics profiling will be used to characterize a broad array of metabolites from plasma in 450 ethnically diverse individuals from Ethiopia, Tanzania, and Botswana with diverse diets. Mass spectrometry will be used to quantify metabolites previously found to be associated with cardiometabolic risk as well as the most informative metabolites from the untargeted screen. We will test for association of selected biomarkers with diet, geography, ancestry, and phenotypic variation. Metabolites obtained will be correlated with diet as well as clinical and anthropometric phenotypes. Using existing tools, we will assemble metabolites that associate with the various phenotypes into pathways and larger networks to provide insights into factors that relate to cardiometabolic health and disease. Finally, we will integrate metabolic and phenotypic data with genetic data from the SNP array and with high coverage whole genome sequence data. We will identify loci that play a role in local adaptation to diverse diets and will identify genetic variants associated with metabolite levels (mQTLs) and with the phenotypic traits listed above.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
43
TOTAL_SUBJECTS
450
STUDY_COMMENTS
Targeted mass spectrometry will be used to quantify metabolites previously found to be associated with cardiometabolic risk as well as the most informative metabolites from the untargeted screen. We will test for association of selected biomarkers with diet, geography, ancestry, and phenotypic variation. Metabolites obtained will be correlated with diet as well as clinical and anthropometric phenotypes. Using existing tools, we will assemble metabolites that associate with the various phenotypes into pathways and larger networks to provide insights into factors that relate to cardiometabolic health and disease. Finally, we will integrate metabolic and phenotypic data with genetic data from the SNP array and with high coverage whole genome sequence data. We will identify loci that play a role in local adaptation to diverse diets and will identify genetic variants associated with metabolite levels (mQTLs) and with the phenotypic traits listed above.
Looking for changes in lipid levels with knock out of ACADM (shACADM)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
GSC 8-11 cells (20 million) were transduced with lentivirus coding for shACADM 4, 6, or scr (control). ACADM is an enzyme responsible for the metabolism of medium chain fatty acids (C4-C12). A round of selection was performed using puromycin to ensure only cells that had been transduced survived. Knockdown of ACADM was confirmed via western blot. Pellets were collected by centrifuging cells for 10 min at max speed. The pellets were washed and each sample was split into quadruplicate.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
2 hydroxyglutarate prodution in neurospheres from IDH1 mouse glioma model #2
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Evaluation of 2HG and a-ketoglutarate in tumor neurospheres (NS) genertated from the mice brain tumors haboring specific genetic lesions: NRAS overexpression, p53 knockdown plus or minus IDH1 mutated and ATRX knockdown.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We are interested in using both spontaneous and stimulated Raman microscopy to visualize these metabolomic changes as spectral alterations. We have two isogneic cell lines of normal human astrocytes differing only by a point mutation in the IDH-1 gene. We will work with the metabolomics core to elucidate the changes in central metabolism and lipid synthesys in an effort to determine the precise biochemical alterations underlying observed spectral differences. We wil then use a selective inhibitor of the IDH1 R132H to demonstrate to attempt to return TCA metabolome and lipidome to WT phenotype. Lastly, we will use a cell-permeablized variant of 2HG (2R-octyl-alpha-hydroxyglutarate) to recaptitulate the R132H mutant phenotype in wild-type cells, providing strong evidence that 2HG accumulation uderlies the metabolomic (and thus, spectral) changes observed.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
2
TOTAL_SUBJECTS
3
STUDY_COMMENTS
The IDH-1 R132H mutation in low grade gliomas preceptitates oncogenesis through a neomorphic enzyme function: the reduction of alpha-ketoglutarate (aKG) to 2-hydroxygutarate (2HG). 2HG accumukates to extremely high (~100mM) concentrations in IDH1 mutant cells and has substantial, predictable metabolic effects, including inhibition of a-KG dependent dioxygenases and hypermethylation of histones and chromatin.
We are interested in using both spontaneous and stimulated Raman microscopy to visualize these metabolomic changes as spectral alterations. We have two isogneic cell lines of normal human astrocytes differing only by a point mutation in the IDH-1 gene. We will work with the metabolomics core to elucidate the changes in central metabolism and lipid synthesys in an effort to determine the precise biochemical alterations underlying observed spectral differences. We wil then use a selective inhibitor of the IDH1 R132H to demonstrate to attempt to return TCA metabolome and lipidome to WT phenotype. Lastly, we will use a cell-permeablized variant of 2HG (2R-octyl-alpha-hydroxyglutarate) to recaptitulate the R132H mutant phenotype in wild-type cells, providing strong evidence that 2HG accumulation uderlies the metabolomic (and thus, spectral) changes observed.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolic profiling of cyst fluid from patients with Intraductal Pancreatic Mucinous Neoplasm
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The pancreatic cyst fluids were collected using a syringe aspiration of the cyst fluid immediately after surgical resection of the lesion. The cyst fluid were then aliquoted and stored in -80C freezer until ready to use. We plan on performing untargeted metabolomics analysis and unknown lipid analysis and identification on these pancreatic cyst fluid to find potential biomarkers that correlate with histopathological assessment and clinical behavior of these cystic lesions and thus to guide clinical management of patients. Abbreviations: IPMN - Intraductal Pancreatic Mucinous Neoplasm; MCN - mucinous cystic neoplasm; SCA - serous cystadenoma.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
SJGBM2 and MGG8 glioma cells were stable transfected with IDH1-R132H mutated. The expression of IDH1-R132H was confirmed by Western Blot assay. The aim of this project is analyze the production of 2HG in the stable transfected cells (SJGBM-IDH1m and MGG8-IDH1m) compared with the control group WT.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Human cord blood serum samples (200) were provided by David Christiani. The 200 study samples, total pool samples, and external CHEAR Plasma Reference Material samples were prepared and analyzed using the Biocrates AbsoluteIDQ p180 Kit.
Metabolic analysis of Normal Mouse Lung Fiboblasts with/without TGFbeta treatment
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Glycolysis/TCA/Nucleotide analysis (especially interested in alpha-ketoglutarate) and NAD+ and related metabolite analysis for parp1 ko and parp1 wild type lung tissue after saline or bleomycin treatment
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We are interested in understanding the bile acid profiles from the feces of fecal microbiota transplant FMT patients that successfully recover from recurrent C. difficile infection. We have are submitting fecal samples from patients prior to their FMT and post FMT. We are also interested in the bile acid profiles of the donor stool that is used in successful transplants. Bile acids are important for C. difficile spore germination and outgrowth.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Detachments were created in adult male Brown-Norway rats (300?400 g; Charles River Laboratories, Wilmington, MA). Briefly, rodents were anesthetized with a 50:50 mix of ketamine/xylazine, and pupils were dilated with topical phenylephrine (2.5%) and tropicamide (1%). A 20-gauge microvitreoretinal blade was used to create a sclerotomy 2 mm posterior to the limbus, carefully avoiding lens damage. A subretinal injector (Glaser, 32-gauge tip; BD Ophthalmic Systems, Franklin Lakes, NJ) was introduced through the sclerotomy into the vitreous cavity and then through a peripheral retinotomy into the subretinal space. Sodium hyaluronate (10 mg/mL, Healon OVD; Abbott Medical Optics, Uppsala, Sweden) was slowly injected to detach the neurosensory retina from the underlying RPE. In all experiments, approximately one third to one half of the neurosensory retina was detached. Detachments were created in the left eye. The right eye served as the control, with all the steps of the procedure performed except for introduction of the subretinal injector and injection of the sodium hyaluronate. At varying intervals after creation of the detachment, the animals were euthanatized, and the eyes were enucleated.The retina was then dissected away from the retinal pigment epithelium taking just the detached portion in those eyes experimentally detached. All experiments were performed in accordance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research and the guidelines established by the University Committee on Use and Care of Animals of the University of Michigan.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
6.5 X 10^6 cells were plated in 10 cm Tissue Culture dishes and allowed to recover overnight at 37 degrees and 5% CO2. In the am, supernatant was removed, and 12 mL of medium containing either Murine Norovirus-1 (MNV) at an MOI=5 or medium containing a v/v match of mock lysate was added to the cells. Plates were rocked on ice for 1 hour, then cells were washed 3X with cold DPBS++, and plain medium as added to cells. Plates were then incubated for 7.5 hours at 37 degrees and 5% CO2. Cells were washed with 12 mL of 150 mM Ammonium Acetate, swirled 8 times, and immediately quenched with liquid nitrogen. Cells were then frozen at -80 degrees.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
2
TOTAL_SUBJECTS
1
STUDY_COMMENTS
BIOHAZARD - MURINE NOROVIRUS - SHOULD BE ENTIRELY NON-INFECTIOUS DUE TO THE LIQUID NITROGEN, BUT PLEASE HANDLE AND DISPOSE OF IN BIOHAZARD WASTE. IMPORTANT NOTE: I request that the metabolites of the TCA+ assay that are to be assessed quantitatively please be sure to include ATP, ADP, AMP, NAD, NADH, NADP, NADPH, E4P, S7P, 6PG, G3P H6P and Lactate. Also, I would request that both reduced and oxidized Glutathione as well as Fructose 1,6-bisphosphate be included in the non-quantitative data.
Purine and TCA measurements in salt sensitive (SS) hypertension
STUDY_TYPE
MS analysis
STUDY_SUMMARY
SS rats were surgically implanted with a chronic servo-control cuff, the purpose of which is to maintain normal pressure to the left kidney while the right kidney is exposed to high blood pressure. After 7 days of high salt treatment, which induces high blood pressure in the SS rat, rats were anesthetized with pentobarbital, kidneys were flushed and removed. The renal medulla was separated from the cortex using scissors, and the renal medullas were frozen in liquid nitrogen and stored at -80 C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Deubiquitinase inhibitor compound C6 effect on cellular metabolism
STUDY_TYPE
MS analysis
STUDY_SUMMARY
6.0 X 10^6 cells were plated in 10 cm Tissue Culture dishes and allowed to recover overnight at 37 degrees and 5% CO2. In the am, supernatant was removed, and 12 mL of fresh medium with either 2.5 micromolar Compound C6 or a v/v match of DMSO (vehicle control) was added to the cells. Cells were incubated at 37 degrees in 5% CO2 for 30 minutes. Cells were washed 3X with cold DPBS++ and 10 mL of medium was added to the cells with either 1.0 micromolar Compound C6 or v/v match of DMSO. Cells were incubated at 37 degrees and 5% CO2 for 7.0 hours. Cells were washed with 10 mL of 150 mM Ammonium Acetate, swirled, washed again with 5 mL, and immediately quenched with liquid nitrogen. Cells were then frozen at -80 degrees.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
7
TOTAL_SUBJECTS
1
STUDY_COMMENTS
I request that the metabolites of the TCA+ assay that are to be assessed quantitatively please be sure to include ATP, ADP, AMP, NAD, NADH, NADP, NADPH, E4P, S7P, 6PG, G3P, H6P, and Lactate in particular. Also, I would request that both reduced and oxidized Glutathione as well as Fructose 1,6-bisphosphate be included in the non-quantitative data.
Pilot Human Muscle oral glucose tolerance test (OGTT)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Obesity is associated with metabolic inflexibility, the inability to switch from lipid to glucose oxidation during physiological conditions favoring excess glucose and insulin, which could contribute to the increased incidence of type 2 diabetes. Despite this knowledge, the role of skeletal muscle metabolites during these physiological conditions remain unclear and warrant further investigation. The purpose of this pilot study is to determine if: 1) there are differences in skeletal muscle glycolysis and TCA metabolites and amino acids between lean and obese individuals in the fasted state, and 2) if these metabolites change after 50 min of glucose ingestion, and 3) if there are differences in these metabolites between lean and obese individuals after 50 min of glucose ingestion.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
In the first group of samples, we are looking into the different metabolites and their concentrations within our human embryonic stem cells over the course of differentiation. Our goal is to study how the metabolism of stem cells are changing as they undergo this conversion to become hepatocyte-like cells. In the second group of samples labeled HyCell, we would like to understand the concentrations of metabolites within our CHO cells in order to update the parameters for our metabolic model. Included are two samples from different days of a suspension batch culture which may have different lactate production qualities.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Obesity and marrow and marrow adipose tissue (MAT) metabolomics
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Male C57Bl6j mice were fed HFD for 16-20 weeks and marrow adipose tissue (MAT) and bone marrow collected to evaluate lipid content/lipid type. In addition, marrow evaluations for glycolysis/TCA cycle and acylcarnitines will be performed.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Effect of cooling on muscle tissue metabolism (part II)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Thermal modalities are commonly used in sports medicine to affect tissue healing. Cold therapy is commonly used modalities, but the metabolic changes to muscle after cooling are not known. The objective of this study is to look at the effect of cooling on muscle metabolites and gene expression. There are a total of 8 subjects in the study. Each subject had an ice cup cryotherapy treatment (cool samples) to one leg for 15 minutes, and the other leg served as the control (cntrl samples). Two hours after the application of cryotherapy, a biopsy was taken from each thigh muscle. Muscle was minced with scissors and quickly snap frozen in liquid nitrogen.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
10
TOTAL_SUBJECTS
8
STUDY_COMMENTS
We would like to run the TCA Plus Analysis on each of the samples. For the statistical analysis, we would normalize the cool side to the ctrl side, and look at the relative change in metabolite abundance as a result of the cooling procedure. only used in sports medicine to affect tissue healing.
Diabetic heart adrenergic signaling and metabolism (STZ & Isoproterenol, High Fat)
STUDY_TYPE
MS analysis
STUDY_SUMMARY
We are examing the effect of both diabetes and adrenergic activation on the metabolomic profile. STZ treatment was initiated 5 months before hearts were harvested. High fat/low fat diets were given for 13 weeks. All hearts were excised in the morning. For the STZ/isoproterenol experiment, mouse anesthesia was initiated with 4% isoflurane, and maintained with 2% and a homeothermic controller. After 5 min of equilibration, control and fasted mice were injected intraperitoneally with either saline (S) or 25ug/kg isoproterenol (I). After an additional 5 min, the whole heart was quickly excised, washed with ice-cold distilled water, dried off with a chem whipe, and flash frozen in liquid nitrogen. Hearts were stored at -80, and shipped using dry ice. The hearts from the high fat diet experiement were prepared in the same way, but no injection was given and total anesthesia time was 5min instead of 10min.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomics of muscle in insulin sensitive and resistant obese indivduals.
STUDY_TYPE
MS analysis
STUDY_SUMMARY
OC samples: muscle biopsy samples collected from insulin sensitive / insulin resistant obese indivduals before undergoing a hyperinsulinemic-euglycemic clamp. Subjects were previously categorized for the rate of fatty acid release from adipose tissue into the bloodstream as a measure of insuline resistance. Low-FA, Med-FA, and High-FA stand for low, medium, and high rate of release.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
PA samples: matched plasma and muscle samples from an obese subject mild-intensity exercise training study, V1 is the first visit (untrained), V4 is post 3 months training, 1 day after exercise and V5 is post 3 months training, 3 days after last exercise.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Innovative and novel therapies are urgently needed for the treatment of patients with severe asthma, especially those who are refractory to standard-of-care bronchodilators and inhaled corticosteroids. The Zeki lab is investigating the role of the mevalonate (MA) pathway, in the pathogenesis of airway inflammation and remodeling. Although statins all inhibit HMGCR in the same manner in terms of enzyme binding site, the statins’ varied physiochemical properties with respect to their polarity (i.e. lipophilicity) result in very different immune and lipid effects. The major significance of this work is to advance a new class of inhaler therapies for asthma; the statins which work by an entirely different mechanism than current ICS/LABA mainstays. Evidence suggests that statins may have an additive benefit to corticosteroids in asthma, thereby confirming a unique mechanism, namely via MVA pathway inhibition. This becomes particularly important in the severe asthma population which is highly corticosteroid-resistant, is poorly controlled with high exacerbation rates and hospitalizations, and has the highest healthcare costs of all asthma phenotypes. In essence, the potential public health impact of even an incremental improvement in asthma symptom control cannot be underestimated. Even the prevention of 1 asthma attack preserves lung function and reduces the adverse personal and financial impact. This study aimed to determine if statin polarity affects airway drug concentration and systemic drug absorption and to determine the effect of inhaled statins on naïve airway immune cell populations and alveolar-capillary membrane and epithelial barrier integrity in healthy rhesus monkeys. In this particular component of the study, we investigated the metabolic effects resulting from the use of statins in these healthy rhesus monkeys. Specifically, the Newman lab analyzed for lipid mediator (oxylipin, endocannabinoid, fatty acid, and nitro lipid) in lung and trachea tissue, plasma, and BAL and bile acid changes in the lung and trachea tissue and plasma.
Innovative and novel therapies are urgently needed for the treatment of patients with severe asthma, especially those who are refractory to standard-of-care bronchodilators and inhaled corticosteroids. The Zeki lab is investigating the role of the mevalonate (MA) pathway, in the pathogenesis of airway inflammation and remodeling. Although statins all inhibit HMGCR in the same manner in terms of enzyme binding site, the statins’ varied physiochemical properties with respect to their polarity (i.e. lipophilicity) result in very different immune and lipid effects. The major significance of this work is to advance a new class of inhaler therapies for asthma; the statins which work by an entirely different mechanism than current ICS/LABA mainstays. Evidence suggests that statins may have an additive benefit to corticosteroids in asthma, thereby confirming a unique mechanism, namely via MVA pathway inhibition. This becomes particularly important in the severe asthma population which is highly corticosteroid-resistant, is poorly controlled with high exacerbation rates and hospitalizations, and has the highest healthcare costs of all asthma phenotypes. In essence, the potential public health impact of even an incremental improvement in asthma symptom control cannot be underestimated. Even the prevention of 1 asthma attack preserves lung function and reduces the adverse personal and financial impact. This study aimed to determine if statin polarity affects airway drug concentration and systemic drug absorption and to determine the effect of inhaled statins on naïve airway immune cell populations and alveolar-capillary membrane and epithelial barrier integrity in healthy rhesus monkeys. In this particular component of the study, we investigated the metabolic effects resulting from the use of statins in these healthy rhesus monkeys. Specifically, the Newman lab analyzed for lipid mediator (oxylipin, endocannabinoid, fatty acid, and nitro lipid) in lung and trachea tissue, plasma, and BAL and bile acid changes in the lung and trachea tissue and plasma.
Innovative and novel therapies are urgently needed for the treatment of patients with severe asthma, especially those who are refractory to standard-of-care bronchodilators and inhaled corticosteroids. The Zeki lab is investigating the role of the mevalonate (MA) pathway, in the pathogenesis of airway inflammation and remodeling. Although statins all inhibit HMGCR in the same manner in terms of enzyme binding site, the statins’ varied physiochemical properties with respect to their polarity (i.e. lipophilicity) result in very different immune and lipid effects. The major significance of this work is to advance a new class of inhaler therapies for asthma; the statins which work by an entirely different mechanism than current ICS/LABA mainstays. Evidence suggests that statins may have an additive benefit to corticosteroids in asthma, thereby confirming a unique mechanism, namely via MVA pathway inhibition. This becomes particularly important in the severe asthma population which is highly corticosteroid-resistant, is poorly controlled with high exacerbation rates and hospitalizations, and has the highest healthcare costs of all asthma phenotypes. In essence, the potential public health impact of even an incremental improvement in asthma symptom control cannot be underestimated. Even the prevention of 1 asthma attack preserves lung function and reduces the adverse personal and financial impact. This study aimed to determine if statin polarity affects airway drug concentration and systemic drug absorption and to determine the effect of inhaled statins on naïve airway immune cell populations and alveolar-capillary membrane and epithelial barrier integrity in healthy rhesus monkeys. In this particular component of the study, we investigated the metabolic effects resulting from the use of statins in these healthy rhesus monkeys. Specifically, the Newman lab analyzed for lipid mediator (oxylipin, endocannabinoid, fatty acid, and nitro lipid) in lung and trachea tissue, plasma, and BAL and bile acid changes in the lung and trachea tissue and plasma.
Innovative and novel therapies are urgently needed for the treatment of patients with severe asthma, especially those who are refractory to standard-of-care bronchodilators and inhaled corticosteroids. The Zeki lab is investigating the role of the mevalonate (MA) pathway, in the pathogenesis of airway inflammation and remodeling. Although statins all inhibit HMGCR in the same manner in terms of enzyme binding site, the statins’ varied physiochemical properties with respect to their polarity (i.e. lipophilicity) result in very different immune and lipid effects. The major significance of this work is to advance a new class of inhaler therapies for asthma; the statins which work by an entirely different mechanism than current ICS/LABA mainstays. Evidence suggests that statins may have an additive benefit to corticosteroids in asthma, thereby confirming a unique mechanism, namely via MVA pathway inhibition. This becomes particularly important in the severe asthma population which is highly corticosteroid-resistant, is poorly controlled with high exacerbation rates and hospitalizations, and has the highest healthcare costs of all asthma phenotypes. In essence, the potential public health impact of even an incremental improvement in asthma symptom control cannot be underestimated. Even the prevention of 1 asthma attack preserves lung function and reduces the adverse personal and financial impact. This study aimed to determine if statin polarity affects airway drug concentration and systemic drug absorption and to determine the effect of inhaled statins on naïve airway immune cell populations and alveolar-capillary membrane and epithelial barrier integrity in healthy rhesus monkeys. In this particular component of the study, we investigated the metabolic effects resulting from the use of statins in these healthy rhesus monkeys. Specifically, the Newman lab analyzed for lipid mediator (oxylipin, endocannabinoid, fatty acid, and nitro lipid) in lung and trachea tissue, plasma, and BAL and bile acid changes in the lung and trachea tissue and plasma.
Innovative and novel therapies are urgently needed for the treatment of patients with severe asthma, especially those who are refractory to standard-of-care bronchodilators and inhaled corticosteroids. The Zeki lab is investigating the role of the mevalonate (MA) pathway, in the pathogenesis of airway inflammation and remodeling. Although statins all inhibit HMGCR in the same manner in terms of enzyme binding site, the statins’ varied physiochemical properties with respect to their polarity (i.e. lipophilicity) result in very different immune and lipid effects. The major significance of this work is to advance a new class of inhaler therapies for asthma; the statins which work by an entirely different mechanism than current ICS/LABA mainstays. Evidence suggests that statins may have an additive benefit to corticosteroids in asthma, thereby confirming a unique mechanism, namely via MVA pathway inhibition. This becomes particularly important in the severe asthma population which is highly corticosteroid-resistant, is poorly controlled with high exacerbation rates and hospitalizations, and has the highest healthcare costs of all asthma phenotypes. In essence, the potential public health impact of even an incremental improvement in asthma symptom control cannot be underestimated. Even the prevention of 1 asthma attack preserves lung function and reduces the adverse personal and financial impact. This study aimed to determine if statin polarity affects airway drug concentration and systemic drug absorption and to determine the effect of inhaled statins on naïve airway immune cell populations and alveolar-capillary membrane and epithelial barrier integrity in healthy rhesus monkeys. In this particular component of the study, we investigated the metabolic effects resulting from the use of statins in these healthy rhesus monkeys. Specifically, the Newman lab analyzed for lipid mediator (oxylipin, endocannabinoid, fatty acid, and nitro lipid) in lung and trachea tissue, plasma, and BAL and bile acid changes in the lung and trachea tissue and plasma.
Targeting Myelin NEFA of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI
STUDY_SUMMARY
Targeting mouse myelin NEFA of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 9 samples total in Project 1, n=3 for each genotype (control, PAR1 or PAR2) at 21 days. There are 9 samples total in Project 2, n=3 for each genotype (WT, PAR1-/- or PAR2-/-) at 60 days. There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeting Myelin FFA Compostion of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI
STUDY_SUMMARY
Targeting mouse myelin FFA composition of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 9 samples total in Project 1, n=3 for each genotype (control, PAR1 or PAR2) at 21 days. There are 9 samples total in Project 2, n=3 for each genotype (WT, PAR1-/- or PAR2-/-) at 60 days. There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeting Myelin Cholesterol of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI
STUDY_SUMMARY
Targeting mouse myelin Cholesterol of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 9 samples total in Project 1, n=3 for each genotype (control, PAR1 or PAR2) at 21 days. There are 9 samples total in Project 2, n=3 for each genotype (WT, PAR1-/- or PAR2-/-) at 60 days. There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeting Myelin Sphingolipids of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI
STUDY_SUMMARY
Targeting Myelin Sphingolipids of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 9 samples total in Project 1, n=3 for each genotype (control, PAR1 or PAR2) at 21 days. There are 9 samples total in Project 2, n=3 for each genotype (WT, PAR1-/- or PAR2-/-) at 60 days. There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeting Myelin Galactosyl Sphingolipids of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI
STUDY_SUMMARY
Targeting mouse myelin Galactosyl Shingolipids of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 9 samples total in Project 1, n=3 for each genotype (control, PAR1 or PAR2) at 21 days. There are 9 samples total in Project 2, n=3 for each genotype (WT, PAR1-/- or PAR2-/-) at 60 days. There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
INSTITUTE
Mayo Clinic
LAST_NAME
Scarisbrick
FIRST_NAME
Isobel
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Targeting Myelin Sphinomyelin concentrations of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI
STUDY_SUMMARY
Targeting Mouse Myelin Sphingomyelin concentrations of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 9 samples total in Project 1, n=3 for each genotype (control, PAR1 or PAR2) at 21 days. There are 9 samples total in Project 2, n=3 for each genotype (WT, PAR1-/- or PAR2-/-) at 60 days. There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
Targeted FFA Composition in Kallikrein 6 Mice after SCI
STUDY_SUMMARY
Targeted FFA Composition in Kallikrein 6 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
Targeted NEFA in Kallikrein 6 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
Targeted Cholesterol Profiling of Myelin to Enhance Recovery of Function after SCI. Second Set of Samples
STUDY_SUMMARY
Tissue is from adult mouse spinal cord (SC). We are submitting these samples for Untargeted Profiling (unbiased metabolomics assay) and for lipid analysis. The lipid assays we request are 1) free fatty acid composition of lipids; 2) free fatty acid panel; 3) cholesterol concentration (free and bound); 4) Ceramides, including galactosyl and glucosyl; 5) sphingomyelin. The Untargeted profiling is our top priority, followed by the lipid assays as listed. All samples were snap frozen at the point of harvest and approximate weights are provided. The samples are submitted as intact pieces of tissue. There are 20 samples total, n=5 for each group that includes LF (low fat diet); HF (high fat diet); HFHS (high fat high sucrose diet); and Keto (ketogenic diet).
Targeted Sphingolipids in Kallikrein 6 Mice after SCI
STUDY_SUMMARY
Targeted Sphingolipids in Kallikrein 6 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
Targeted Galactosyl Sphingolipid Concentration in Kallikrein 6 Mice after SCI
STUDY_SUMMARY
Targeted Galactosyl Sphingolipids in Kallikrein 6 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
Targeted Sphingomyelin Concentrations in Kallikrein 6 Mice after SCI
STUDY_SUMMARY
Targeted Sphingomyelin in Kallikrein 6 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
Targeting Myelin NEFA in PAR1 and PAR2 Mice after SCI
STUDY_SUMMARY
Targeting Myelin NEFA in PAR1 and PAR2 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21 or 60 mouse spinal cord (SC). There are 30 total sampes, n=5 for each group. wild type control, PAR1 KO and PAR2 KO at P21 and P60 days.
Targeting Myelin FFA Compostion in PAR1 and PAR2 Mice after SCI
STUDY_SUMMARY
Targeting Myelin FFA composition in PAR1 and PAR2 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21 or 60 mouse spinal cord (SC). There are 30 total sampes, n=5 for each group. wild type control, PAR1 KO and PAR2 KO at P21 and P60 days.
Targeting Myelin Cholesterol in PAR1 and PAR2 Mice after SCI
STUDY_SUMMARY
Targeting Myelin Cholesterol in PAR1 and PAR2 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21 or 60 mouse spinal cord (SC). There are 30 total sampes, n=5 for each group. wild type control, PAR1 KO and PAR2 KO at P21 and P60 days.
Targeting Myelin Ceramides in PAR1 and PAR2 Mice after SCI
STUDY_SUMMARY
Targeting Myelin ceramides in PAR1 and PAR2 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21 or 60 mouse spinal cord (SC). There are 30 total sampes, n=5 for each group. wild type control, PAR1 KO and PAR2 KO at P21 and P60 days.
Identification of Race-Associated Metabolite Biomarkers for Hepatocellular Carcinoma
STUDY_SUMMARY
Introduction: Metabolomics provides simultaneous assessment of a broad range of metabolites that can potentially serve as indicators of the overall physiology status as well as the response to host and environmental stimuli. It has been broadly used for biomarker discovery and characterization of complex diseases such as cancer. The evaluation of the changes in the levels of metabolites in samples stratified by race could lead to the identification of more reliable biomarkers than those obtained through whole-population-based approaches. In this study, we used plasma samples collected from patients recruited at MedStar Georgetown University Hospital to investigate metabolites that may be associated with hepatocellular carcinoma (HCC) in a race-specific manner. Methods: Plasma samples were protein depleted using a solution composed of acetonitrile:isopropanol:water (3:3:2) containing a mixture of isotope-labeled internal standards. The extracted metabolites were trimethylsilyl derivatized prior to analysis by GC-MS. A quality control (QC) sample derived by pooling plasma from multiple subjects was run in between samples to assess reproducibility. A mixture of fatty acids methyl esters (FAMEs) and alkane standards was run for retention index calibration. The mixture of isotope-labeled internal standards was used to evaluate the reproducibility of the GC-MS data across multiple runs. Preliminary Data: Plasma samples collected from 40 HCC cases and 44 patients with liver cirrhosis were analyzed. The cirrhotic controls were frequency matched with the HCC cases by demographic variables. The participants included 19 African Americans (AA) and 50 European Americans (EA). The analysis targeted 46 metabolites for quantitative analysis by Agilent GC-qMS in selected ion monitoring (SIM) mode. The data were pre-processed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) for peak detection, deconvolution, and identification. The resulting peaks were aligned using Mass Profiler Professional (MPP) from Agilent Technologies. A LASSO regression model was applied to select metabolites with significant changes in HCC vs. cirrhosis in three groups: (1) AA and EA combined; (2) AA only; and (3) EA only. Also, metabolites that distinguish HCC cases from cirrhosis in the three groups were selected by considering only those subjects with Hepatitis C virus (HCV) infection. The performances of the metabolites selected by LASSO in each group were evaluated through a leave-one-out cross-validation. We identified race-specific metabolites that differentiated HCC cases from cirrhotic controls, yielding better area under the ROC curve compared to alpha-fetoprotein (AFP) - the serological marker widely used for the diagnosis of HCC. Novel Aspect: We identified race-associated metabolites that are significantly altered in HCC vs. cirrhosis, suggesting the potential role of race in HCC.
INSTITUTE
Georgetown University
DEPARTMENT
Oncology, Georgetown University Medical Center
LABORATORY
Ressom Lab (PI: Habtom W. Ressom, email address hwr@georgetown.edu)
LAST_NAME
Cristina
FIRST_NAME
Di Poto
ADDRESS
3970 Reservoir Rd., NW, Research Bldg, Room W325, Washington, DC, 20007, USA
Large Untargeted Profiling in PAR1 and PAR2 Mice after SCI
STUDY_SUMMARY
Large Untargeted Profiling in NEFA in PAR1 and PAR2 Mice after SCI. The samples submitted are purified myelin preparations from the postnatal day 21 or 60 mouse spinal cord (SC). There are 30 total sampes, n=5 for each group. wild type control, PAR1 KO and PAR2 KO at P21 and P60 days.
In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabotype. Additional samples reflecting different stages of date fruit ripening process has been included for 10 different fruit varieties. This study includes updated date photographs and combined results data (GCMS/LCMS) and technical validation data, see downloadable files section to access this information.
Untargeted metabolomic profile of oak and wine yeast strains
STUDY_SUMMARY
Metabolomic profiles were compiled from oak and wine yeast parents over three extraction times (batch). Included in this study are extraction controls.
INSTITUTE
Washington University in St. Louis
LAST_NAME
Swain Lenz
FIRST_NAME
Devjanee
ADDRESS
4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA
Large Untargeted Profiling in Kallikrein 6 Mice after SCI
STUDY_SUMMARY
Large untargeted profiling mouse myelin of Kallikrein 6 Signals through PAR1 and PAR2 to Enchance Recovery of Function after SCI. The samples submitted are purified myelin preparations from the postnatal day 21, 60, or 90 mouse spinal cord (SC). There are 12 samples total in Project 3, n=3 for K6+/+ or K6-/- at either P21 or P90.
Metabolomic profiles were compiled from reciprocal hemizygotes (oak/win hybrid, genes AUA1, ARG82) (batch). Included in this study are extraction controls.
INSTITUTE
Washington University in St. Louis
LAST_NAME
Swain Lenz
FIRST_NAME
Devjanee
ADDRESS
4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA
Maternal Hypoxemia and oxidative stress in the fetus, newborn, and adult. exercise training for peripheral artery disease
STUDY_TYPE
Disease model
STUDY_SUMMARY
Gestational hypoxia presents a significant stress to an unborn fetus that can lead to significant complications related to fetal growth restriction and resulting in diseases in the newborn as well as those manifesting later in life. Recent evidence indicates that inflammation and oxidative stress are contributing factors to hypoxia-related diseases. The Center for Perinatal Biology at Loma Linda University has studied gestational chronic hypoxia in a sheep model for over 20 years to study dysfunction of vascular and nonvascular tissues derived from mothers, fetuses and offspring. In this project we are attempting to use metabolomics to assess metabolic dysregulation in vascular tissues along with markers of oxidative stress and inflammation in the mother and offspring to determine the extent of dysregulation due to chronic hypoxia. Untargeted metabolomics analysis focused on sheep plasma and arteries from the lung, resistance arteries in the brain, uterine arteries, and cultured human myocytes will be used to explore markers of glucose and lipid metabolism disruption. Targeted analyses of oxylipins and endocannabinoids will be used on the same samples to explore markers of oxidative stress and inflammation, which should be increased during hypoxia. This study should delineate pathways and biomarkers that help explain how hypoxia leads to the development of neonatal as well as adult-onset diseases associated with chronic hypoxia that are inter-related with fetal growth restriction.
Maternal Hypoxemia and oxidative stress in the fetus, newborn, and adult. exercise training for peripheral artery disease (part II)
STUDY_TYPE
Disease model
STUDY_SUMMARY
Gestational hypoxia presents a significant stress to an unborn fetus that can lead to significant complications related to fetal growth restriction and resulting in diseases in the newborn as well as those manifesting later in life. Recent evidence indicates that inflammation and oxidative stress are contributing factors to hypoxia-related diseases. The Center for Perinatal Biology at Loma Linda University has studied gestational chronic hypoxia in a sheep model for over 20 years to study dysfunction of vascular and nonvascular tissues derived from mothers, fetuses and offspring. In this project we are attempting to use metabolomics to assess metabolic dysregulation in vascular tissues along with markers of oxidative stress and inflammation in the mother and offspring to determine the extent of dysregulation due to chronic hypoxia. Untargeted metabolomics analysis focused on sheep plasma and arteries from the lung, resistance arteries in the brain, uterine arteries, and cultured human myocytes will be used to explore markers of glucose and lipid metabolism disruption. Targeted analyses of oxylipins and endocannabinoids will be used on the same samples to explore markers of oxidative stress and inflammation, which should be increased during hypoxia. This study should delineate pathways and biomarkers that help explain how hypoxia leads to the development of neonatal as well as adult-onset diseases associated with chronic hypoxia that are inter-related with fetal growth restriction.
Micronutrient deficiencies, environmental exposures and severe malaria: Risk factors for adverse neurodevelopmental outcomes in Ugandan children
STUDY_TYPE
Untargeted high-resolution mass spectrometry profiling
STUDY_SUMMARY
Micronutrient deficiencies and environmental exposures have been to known to adversely impact brain and nervous system functions in adults and children worldwide. However, few studies have examined the short and long-term impact of these risk factors on neurodevelopmental outcomes in children in low-income countries, where the effects are likely to be more pronounced due to limited resources for monitoring and insufficient regulations. Biological risk factors of relevance include micronutrient deficiencies such as zinc and exposure to heavy metals such as lead and mercury. Studies have suggested an association between neurodevelopmental impairment and micronutrient deficiency as well as exposure to a number of heavy metals and environmental toxins. Moreover, findings also suggest that risk factors for adverse developmental outcomes that are independently significant may have the potential for causing cumulative increases in adverse effects. In Sub-Saharan Africa, severe malaria is a leading risk factor for long-term neurocognitive impairment in children. Zinc deficiency or exposure to heavy metals could influence risk of severe malaria, modify the risk of neurocognitive impairment in children with severe malaria, or independently affect risk of neurocognitive impairment. Untargeted analyses for potential environmental exposures or metabolomic changes in children with cerebral malaria vs. without cognitive impairment or in children with higher vs. lower cognitive scores, could also identify new risk factors for neurodevelopmental impairment in Ugandan children with cerebral malaria.In our completed study in Kampala, we assessed neurologic and developmental impairment in children with cerebral malaria [CM] or severe malarial anemia [SMA], as compared to health community children from the same extended household as the children with CM or SMA. As an extension of this study, we are interested in determining levels of micronutrients such as zinc in the population, and in addition, determining exposure levels of heavy metals (lead, mercury, copper, manganese etc.) in samples collected from children with severe malaria and community controls. The primary hypotheses of this study is that nutrient deficiencies or exposure to heavy metals influence short and long term neurocognitive outcomes in healthy community children and in children with severe malaria, and that children with cerebral malaria have specific metabolomic changes that relate to long-term neurocognitive impairment. The specific aims of our study are:Aim 1: To determine levels of zinc, heavy metals, and biomarkers associated with inflammation in children presenting with different forms of severe malaria (SM) and in healthy community children (CC). The working hypothesis of this aim is that 1) children with SM will have lower zinc levels compared to CC; 2) children with SM will present with higher toxic metal exposure and higher levels of biomarkers associated with inflammation than CC.Aim 2: To investigate how micronutrient deficiency, toxic metal exposure and inflammatory biomarkers affect short and long term neurodevelopmental outcomes and growth in children with severe malaria and community children (CC).The working hypothesis of this aim is that the lower levels of zinc, and presence of toxic metals in high concentrations will independently contribute to worsening neurodevelopmental outcomes and worsening growth over time in children with severe malaria and in community children. An alternate hypothesis is that micronutrient deficiency, toxic metal exposure and inflammatory states may interact with each other and with severe malaria to produce greater neurodevelopmental impairment, i.e., that the contribution is not independent but interactive.Aim 3: To determine whether the CSF metabolome differs according to level of neurodevelopmental impairment in children with cerebral malaria. The working hypothesis of this aim is that neurodevelopmental impairment in children with cerebral malaria is associated with changes in the CSF metabolome.
INSTITUTE
Emory University School of Medicine
DEPARTMENT
Division of Pulmonary, Allergy and Critical Care Medicine
LABORATORY
Clincal Biomarkers Laboratory
LAST_NAME
Walker
FIRST_NAME
Douglas
ADDRESS
615 Michael St. Ste 225, Atlanta, GA, 30322, USA
EMAIL
douglas.walker@emory.edu
PHONE
(404) 727 5984
TOTAL_SUBJECTS
141
STUDY_COMMENTS
CSF pools from elderly individuals included for QA/QC. Study specific pools were not created due to limited sample volumes provided (<100uL).
Fatty Acid Oxidation is Impaired in An Orthologous Mouse Model of Autosomal Dominant Polycystic Kidney Disease
STUDY_SUMMARY
Autosomal Dominant Polycystic Kidney Disease (ADPKD; MIM ID's 173900, 601313, 613095) is estimated to affect almost 1/1000 and is the most common genetic cause of end stage renal disease (Torres et al., 2007). While advances have been made in slowing the progression of some other forms of chronic kidney disease, standard treatments have not reduced the need for renal replacement therapy in ADPKD (Spithoven et al., 2014). Unfortunately, several experimental interventions also have recently failed to show significant benefit in slowing the rate of functional decline (Serra et al., 2010; Walz et al., 2010; Schrier et al., 2014; Torres et al., 2014), and the only positive study reported very modest effects (Torres et al., 2012). These findings suggest new treatment strategies are required. A central dogma of molecular genetics is that discovery of the causative genes will lead to identification of key pathways and potential targets for intervention. In the case of ADPKD, the two genes mutated in the disorder, PKD1 and PKD2, were identified almost 20 years ago and yet their functions remain poorly understood. The PKD1 gene product, polycystin-1 (PC1), encodes a large membrane protein that requires the PKD2 gene product, polycystin-2 (PC2), for its trafficking to the primary cilium where the two are thought to form a receptor channel complex (Kim et al., 2014; Cai et al., 2014). What the complex senses and what it signals remains controversial. The primary cilium has emerged as a key player in the pathogenesis of PKD as mutations in dozens of different genes that encode either essential ciliary components or factors in ciliary signaling pathways result in PKD. A recent report suggests that the relationship between the polycystin complex and ciliary signaling is complicated, however.While ablation of primary cilia by mutation of core ciliary components results in cysts, these same perturbations done in the setting of Pkd1 or Pkd2 inactivation results in significant attenuation of cystic disease (Ma et al., 2013). These data suggest that the polycystin complex provides a suppressive signal for a novel, cilia-dependent growth-promoting pathway that is independent of MAPK/ERK, mTOR, or cAMP pathways, three effector pathways previously implicated as major drivers of cyst growth. The identities of the growth-promoting and growth-inhibiting pathways remain unknown. We have taken a systems-based approach to study Pkd1 gene function. Building on our previous work identifying markedly different outcomes in animals with induced Pkd1 inactivation before or after P12 and correlating this susceptibility with metabolic status (Piontek et al., 2007; Menezes et al., 2012), we now show that female sex is partially protective in adult-induced Pkd1 inactivation, that sex differences in metabolic status may account for this effect, and that cells lacking Pkd1 have abnormal fatty acid oxidation. Finally, manipulating diet in Pkd1 mouse models, we demonstrate a positive correlation between lipid content in mouse chow and cystic kidney disease severity. Our results therefore suggest that abnormal lipid metabolism is an intrinsic component of PKD and an important modifier of disease progression.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Diet, genetics and gut microbiome drive dynamic changes in plasma metabolites [plasma]
STUDY_TYPE
Plasma data
STUDY_SUMMARY
C57BL/6J mice (B6) and 129S1 mice (129J) were purchased from Jackson Laboratory (Bar Harbor, ME) and 129S6 mice (129T) were purchased from Taconic Farms (Germantown, NY). Mice were maintained on normal chow containing 22% calories from fat, 23% from protein and 55% from carbohydrates (Mouse Diet 9F 5020, PharmaServ, Framingham, MA) or a high fat diet (Open Source Diet, D12492, Research Diets, New Brunswick, NJ) containing 60% calories from fat, 20% from protein and 20% from carbohydrates. For antibiotic treatment, 6-week old mice were treated with either placebo, vancomycin (1g/L) or metronidazole (1g/L) (Sigma-Aldrich, St. Louis, MO) in drinking water then started on HFD from age 7 to 11 weeks. The mice were fasted for 2 hours and anesthetized with isoflurane before collecting cecum and plasma.
Diet, genetics and gut microbiome drive dynamic changes in plasma metabolites [cecal]
STUDY_TYPE
Cecal data
STUDY_SUMMARY
C57BL/6J mice (B6) and 129S1 mice (129J) were purchased from Jackson Laboratory (Bar Harbor, ME) and 129S6 mice (129T) were purchased from Taconic Farms (Germantown, NY). Mice were maintained on normal chow containing 22% calories from fat, 23% from protein and 55% from carbohydrates (Mouse Diet 9F 5020, PharmaServ, Framingham, MA) or a high fat diet (Open Source Diet, D12492, Research Diets, New Brunswick, NJ) containing 60% calories from fat, 20% from protein and 20% from carbohydrates. For antibiotic treatment, 6-week old mice were treated with either placebo, vancomycin (1g/L) or metronidazole (1g/L) (Sigma-Aldrich, St. Louis, MO) in drinking water then started on HFD from age 7 to 11 weeks. The mice were fasted for 2 hours and anesthetized with isoflurane before collecting cecum and plasma.
Breathprinting Reveals Malaria-Associated Biomarkers and Mosquito Attractants
STUDY_SUMMARY
Current evidence suggests that malaria infection could alter patient breath metabolites, a phenomenon that could be exploited to create a breath-based diagnostic test. Indications include the preferential attraction of the Anopheles mosquito vector upon infection and a distinct breath profile with the progression of experimental, sub-microscopic malaria. However, these observations have yet to be extended to the clinic. To investigate whether natural human malaria infection leads to a characteristic breath profile, we performed a field study in Malawi. Breath volatiles from pediatric patients with and without uncomplicated falciparum malaria were analyzed by thermal desorption-gas chromatography/mass spectrometry. Using an unbiased, correlation-based analysis, we find that children with malaria have a distinct shift in overall breath composition. Leveraging these differences, highly accurate classification of infection status was achieved with a suite of six compounds. In addition, we find that malaria-infected children have significantly higher breath levels of two mosquito-attractant terpenes, α-pinene and 3-carene. Thus, our work attests to the viability of breath analysis for malaria diagnosis, identifies candidate compounds for follow-up studies, and identifies biologically plausible chemical mediators for increased mosquito attraction to malaria-infected patients.
INSTITUTE
Washington University School of Medicine
LAST_NAME
Schaber
FIRST_NAME
Chad
ADDRESS
4938 Parkview Place, MPRB/FLoor 6, Entry 5, St. Louis, MO, 63110, USA
Evidence that COG0325 proteins are involved in PLP homeostasis
STUDY_SUMMARY
Pyridoxal 5'-phosphate (PLP) is an essential cofactor for nearly 60 Escherichia coli enzymes but is a highly reactive molecule that is toxic in its free form. How PLP levels are regulated and how PLP is delivered to target enzymes are still open questions. The COG0325 protein family belongs to the fold-type III class of PLP enzymes and binds PLP but has no known biochemical activity although it occurs in all kingdoms of life. Various pleiotropic phenotypes of the E. coli COG0325 (yggS) mutant have been reported, some of which were reproduced and extended in this study. Comparative genomic, genetic and metabolic analyses suggest that these phenotypes reflect an imbalance in PLP homeostasis. The E. coli yggS mutant accumulates the PLP precursor pyridoxine 5'-phosphate (PNP) and is sensitive to an excess of pyridoxine but not of pyridoxal. The pyridoxine toxicity phenotype is complemented by the expression of eukaryotic yggS orthologs. It is also suppressed by the presence of amino acids, specifically isoleucine, threonine and leucine, suggesting the PLP-dependent enzyme transaminase B (IlvE) is affected. These genetic results lay a foundation for future biochemical studies of the role of COG0325 proteins in PLP homeostasis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
LB stands for Luria Bertani medium. MG stands for minimal growth For strains grown on MG OD 0.5 is the mid log growth phase and OD 1.0 is the late log growth phase For strains grown on LB OD 1 is the mid log growth phase and OD 2.0 is the late log growth phase
Gut Microbiota Modulate Brain Insulin Sensitivity and Neurobehavior
STUDY_TYPE
Metabolite profiling of cecal contents and brains of mice under diet-induced obesity (DIO) with and without antibiotic treatments.
STUDY_SUMMARY
C57BL/6J mice were purchased from Jackson Laboratory and maintained on either a normal chow containing 22% of calories from fat, 23% from protein, and 55% from carbohydrates (Mouse diet 9F 5020; PharmaServ) or a high-fat diet (Open Source Diet, D12492; Research Diets) containing 60% of calories from fat, 20% from protein, and 20% from carbohydrates for 6 weeks. During the last 2 weeks, some of the HFD mice were treated with vancomycin or metronidazole (1 g/L in the drinking water). All mice were housed at 22°C on a 12 h light/dark cycle. All animal studies were approved by the IACUC of Joslin Diabetes Center (# 97-05) and Harvard Medical School (# 05131) and were in accordance with NIH guidelines. The metabolite profiling was conducted on plasma, hypothalamus and nucleus accumbens.
Mechanism Behind Stay Green Trait in Bread Wheat (Triticum aestivum L.)
STUDY_TYPE
Comparison
STUDY_SUMMARY
Two different wheat genotypes were treated with the high temperature and control conditions under full irrigated condition. Leaf tissues were collected for all 2-different treatments with six replicates after 7 and 10 days of high temperature treatment.
Retrospective serum samples from patients with early Lyme disease, other diseases, and healthy controls were analyzed for small molecule metabolites by liquid chromatography-mass spectrometry (LC-MS). A metabolomics data workflow was applied to select a biosignature for classifying early Lyme disease and non-Lyme disease patients. A statistical model of the biosignature was trained using the patients' LC-MS data, and subsequently applied as an experimental diagnostic tool with LC-MS data from additional patient sera.
INSTITUTE
Colorado State University
DEPARTMENT
MIP
LABORATORY
Belisle
LAST_NAME
Belisle
FIRST_NAME
John
ADDRESS
200 West Lake, Campus Delivery 0922, Colorado State University, Fort Collins, CO, 80523, USA
EMAIL
john.belisle@colostate.edu
PHONE
970-491-5384
NUM_GROUPS
9
STUDY_COMMENTS
All samples and data used in training are provided. All samples and data used in testing are provided, except healthy controls that were experimentally heat treated.
GC-MS analysis of Quercus ilex organs (leaves, roots and acorns)
STUDY_TYPE
Untargeted metabolomics
STUDY_SUMMARY
Qualitative metabolomics study on leaves, roots and acorns from Quercus ilex plantlets. We analyzed polar(metanol:water) and apolar (chloroform) fractions.
INSTITUTE
Universidad de Córdoba
DEPARTMENT
Department Biochemistry and Molecular Biology
LABORATORY
Agroforestry and Plant Biochemistry, Proteomics and Systems Biology
Free fatty acids in mouse plasma were identified and quantified by LC-MS. Through differential feeding and PHZ (phnylhydrazine) dosing, coupled with mass spectrometry, we identified the long chain fatty acid C24:5 as a natural RXRA ligand, which was dynamically increased in concentration in response to hematopoietic stress. Collectively, these data demonstrate that natural RXRA ligands are present and are dynamically regulated in vivo in mouse hematopoietic cells.
Analysis of the effects of Tyrosine Kinase Inhibitors Sunitinib and Erlotinib on Heart, Metabolism In Vivo
STUDY_SUMMARY
Background.More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The tyrosine kinase inhibitor erlotinib targets epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGRF) and platelet-derived growth factor receptor (PDGFR). TKIs impact the function of non-malignant cells had have on- and off-target toxicities, including cardiotoxicities. Most of the reports of sunitinib have identified cardiotoxic effects, whereas erlotinib was less often found to have these effects. We hypothesized that the deleterious effects of TKIs were related to their impact on cardiac metabolism. Methods. C57BL/6 mice (10/group) were treated with therapeutic doses of sunitinib (40 mg/kg), erlotinib (50 mg/kg), or vehicle daily for 2 weeks. Echocardiographic assessment of the heart in vivo identified significant systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Heart, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Results. Compared to vehicle treated controls, sunitinib treated mice had significant decreases insystolic function, whereas erlotinib treated mice did not. Non-Targeted metabolomics analysis of heart identified identified significant decreases in Docosahexaenoic acid (DHA), Arachidonic Acid/Eicosapentaenoic acid (EPA), O-Phosphocolamine, and 6-Hydroxynicotinic acid after sunitinib treatment. DHA was significantly decreased in skeletal muscle (quadriceps femoris), with elevations in cholesterol were identified in liver and elevated ethanol amine in serum. In contrast, erlotinib affected only one metabolite elevated (spermidine significantly increased).Conclusions.Mice treated with sunitinib had exhibited systolic dysfunction within two weeks, with significantly lower heart and skeletal muscle levels of long chain omega-3 fatty acids docosahexaenoic acid (DHA), arachidonic acid (AA)/eicosapentaenoic acid (EPA) and increased serum O-Phosphocholine phospholipid. This is the first link between sunitinib-induced cardiotoxicity and depletion in the polyunsaturated fatty acids (PUFAs) and inflammatory mediators DHA and AA/EPA in the heart, possibly by affecting mitochondria function where they have vital roles on calcium channels.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
919-360-7599
STUDY_COMMENTS
Cardiac tissue, Gastrocnemius Muscle, Liver, and Serum
Analysis of the effects of Tyrosine Kinase Inhibitors Sunitinib and Erlotinib on Liver Metabolism In Vivo
STUDY_SUMMARY
Background.More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The tyrosine kinase inhibitor erlotinib targets epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGRF) and platelet-derived growth factor receptor (PDGFR). TKIs impact the function of non-malignant cells had have on- and off-target toxicities, including cardiotoxicities. Most of the reports of sunitinib have identified cardiotoxic effects, whereas erlotinib was less often found to have these effects. We hypothesized that the deleterious effects of TKIs were related to their impact on cardiac metabolism. Methods. C57BL/6 mice (10/group) were treated with therapeutic doses of sunitinib (40 mg/kg), erlotinib (50 mg/kg), or vehicle daily for 2 weeks. Echocardiographic assessment of the heart in vivo identified significant systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Heart, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Results. Compared to vehicle treated controls, sunitinib treated mice had significant decreases insystolic function, whereas erlotinib treated mice did not. Non-Targeted metabolomics analysis of heart identified identified significant decreases in Docosahexaenoic acid (DHA), Arachidonic Acid/Eicosapentaenoic acid (EPA), O-Phosphocolamine, and 6-Hydroxynicotinic acid after sunitinib treatment. DHA was significantly decreased in skeletal muscle (quadriceps femoris), with elevations in cholesterol were identified in liver and elevated ethanol amine in serum. In contrast, erlotinib affected only one metabolite elevated (spermidine significantly increased).Conclusions.Mice treated with sunitinib had exhibited systolic dysfunction within two weeks, with significantly lower heart and skeletal muscle levels of long chain omega-3 fatty acids docosahexaenoic acid (DHA), arachidonic acid (AA)/eicosapentaenoic acid (EPA) and increased serum O-Phosphocholine phospholipid. This is the first link between sunitinib-induced cardiotoxicity and depletion in the polyunsaturated fatty acids (PUFAs) and inflammatory mediators DHA and AA/EPA in the heart, possibly by affecting mitochondria function where they have vital roles on calcium channels.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
919-360-7599
STUDY_COMMENTS
Cardiac tissue, Gastrocnemius Muscle, Liver, and Serum
Analysis of the effects of Tyrosine Kinase Inhibitors Sunitinib and Erlotinib on Serum Metabolism In Vivo using Non-Targeted Metabolomics Analysis
STUDY_SUMMARY
Background.More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The tyrosine kinase inhibitor erlotinib targets epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGRF) and platelet-derived growth factor receptor (PDGFR). TKIs impact the function of non-malignant cells had have on- and off-target toxicities, including cardiotoxicities. Most of the reports of sunitinib have identified cardiotoxic effects, whereas erlotinib was less often found to have these effects. We hypothesized that the deleterious effects of TKIs were related to their impact on cardiac metabolism. Methods. C57BL/6 mice (10/group) were treated with therapeutic doses of sunitinib (40 mg/kg), erlotinib (50 mg/kg), or vehicle daily for 2 weeks. Echocardiographic assessment of the heart in vivo identified significant systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Heart, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Results. Compared to vehicle treated controls, sunitinib treated mice had significant decreases insystolic function, whereas erlotinib treated mice did not. Non-Targeted metabolomics analysis of heart identified identified significant decreases in Docosahexaenoic acid (DHA), Arachidonic Acid/Eicosapentaenoic acid (EPA), O-Phosphocolamine, and 6-Hydroxynicotinic acid after sunitinib treatment. DHA was significantly decreased in skeletal muscle (quadriceps femoris), with elevations in cholesterol were identified in liver and elevated ethanol amine in serum. In contrast, erlotinib affected only one metabolite elevated (spermidine significantly increased).Conclusions.Mice treated with sunitinib had exhibited systolic dysfunction within two weeks, with significantly lower heart and skeletal muscle levels of long chain omega-3 fatty acids docosahexaenoic acid (DHA), arachidonic acid (AA)/eicosapentaenoic acid (EPA) and increased serum O-Phosphocholine phospholipid. This is the first link between sunitinib-induced cardiotoxicity and depletion in the polyunsaturated fatty acids (PUFAs) and inflammatory mediators DHA and AA/EPA in the heart, possibly by affecting mitochondria function where they have vital roles on calcium channels.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
919-360-7599
STUDY_COMMENTS
Cardiac tissue, Gastrocnemius Muscle, Liver, and Serum
Analysis of the effects of Tyrosine Kinase Inhibitors Sunitinib and Erlotinib on Muscle Metabolism In Vivo
STUDY_SUMMARY
Background.More than 90 tyrosine kinases have been implicated in the pathogenesis of malignant transformation and tumor angiogenesis. Tyrosine kinase inhibitors (TKIs) have emerged as effective therapies in treating cancer by exploiting this kinase dependency. The tyrosine kinase inhibitor erlotinib targets epidermal growth factor receptor (EGFR), whereas sunitinib targets primarily vascular endothelial growth factor receptor (VEGRF) and platelet-derived growth factor receptor (PDGFR). TKIs impact the function of non-malignant cells had have on- and off-target toxicities, including cardiotoxicities. Most of the reports of sunitinib have identified cardiotoxic effects, whereas erlotinib was less often found to have these effects. We hypothesized that the deleterious effects of TKIs were related to their impact on cardiac metabolism. Methods. C57BL/6 mice (10/group) were treated with therapeutic doses of sunitinib (40 mg/kg), erlotinib (50 mg/kg), or vehicle daily for 2 weeks. Echocardiographic assessment of the heart in vivo identified significant systolic dysfunction consistent with cardiotoxicity compared to vehicle treated controls. Heart, skeletal muscle, liver, and serum were flash frozen and prepped for non-targeted GC-MS metabolomics analysis. Results. Compared to vehicle treated controls, sunitinib treated mice had significant decreases insystolic function, whereas erlotinib treated mice did not. Non-Targeted metabolomics analysis of heart identified identified significant decreases in Docosahexaenoic acid (DHA), Arachidonic Acid/Eicosapentaenoic acid (EPA), O-Phosphocolamine, and 6-Hydroxynicotinic acid after sunitinib treatment. DHA was significantly decreased in skeletal muscle (quadriceps femoris), with elevations in cholesterol were identified in liver and elevated ethanol amine in serum. In contrast, erlotinib affected only one metabolite elevated (spermidine significantly increased).Conclusions.Mice treated with sunitinib had exhibited systolic dysfunction within two weeks, with significantly lower heart and skeletal muscle levels of long chain omega-3 fatty acids docosahexaenoic acid (DHA), arachidonic acid (AA)/eicosapentaenoic acid (EPA) and increased serum O-Phosphocholine phospholipid. This is the first link between sunitinib-induced cardiotoxicity and depletion in the polyunsaturated fatty acids (PUFAs) and inflammatory mediators DHA and AA/EPA in the heart, possibly by affecting mitochondria function where they have vital roles on calcium channels.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
919-360-7599
STUDY_COMMENTS
Cardiac tissue, Gastrocnemius Muscle, Liver, and Serum
Untargeted metabolomics analysis of ischemia-reperfusion injured hearts ex vivo from sedentary and exercise trained rats.
STUDY_SUMMARY
The effects of exercise on the heart and its resistance to disease are well-documented. Recent studies have identified exercise-induced resistance to arrhythmia is due to the preservation of mitochondrial membrane potential. To identify novel metabolic changes that occurred parallel to these mitochondrial alterations, we performed non-targeted metabolomics analysis on hearts from sedentary (Sed) and exercise- trained (Ex) rats challenged with isolated heart ischemia-reperfusion injury (I/R). Eight weeks old Sprague- Dawley rats were treadmill trained five days/week for six weeks (exercise duration and intensity progressively increased to 1 hour at 30 m/min up to 10.5% incline, 75-80% VO2mx). The recovery of pre-ischemic function for sedentary rat hearts was 28.8+/-5.4% (N=12) compared to exercise trained hearts which recovered 51.9%+/-5.7 (N=14)(p<0.001). Non-targeted GC-MS metabolomics analysis of 1) Sedentary rat hearts; 2) Exercise-trained rat hearts; 3) Sedentary rat hearts challenged with global ischemia-reperfusion (I/R) injury; and 4) Exercise-trained rat hearts challeged with global I/R (10/group) revealed 20 statistically significant metabolites between groups by ANOVA using Metaboanalyst (p<0.001). Enrichment analysis of these metabolites for pathway-associated metabolic sets indicated a >10 fold enrichment for ammonia recycling and protein biosynthesis (L-Glutamic acid; L-Proline; L-Histidine; L-Serine; L-Aspartic acid; L-Glutamine)(p<=4.05E-05, FDR=0.0024). Subsequent comparison of the sedentary hearts post-I/R and exercise-trained hearts post-I/R further identified significant differences in metabolites related to Aminoacyl-tRNA biosynthesis and nitrogen metabolism (4) (p<=1.24E-05, FDR<=5.07E-4). These studies shed light on novel mechanisms in which exercise-induced cardioprotection occurs in I/R which complement both the mitochondrial stabilization and antioxidant mechanisms recently described. These findings also link protein synthesis and protein degradation (protein quality control mechanisms) with exercise-linked cardioprotection and mitochondrial susceptibility for the first time in cardiac I/R.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
TAp73 is a marker of glutamine addiction in medulloblastoma
STUDY_TYPE
siRNA constructs targeting p73 (ID: 2671-AMBION) and a non-targeting control siRNA (scramble) were transfected with 10 pM siRNA with lipofectamine 3000 according to the supplier’s protocol for 48 hours
STUDY_SUMMARY
Metabolically-targeted therapies hold the promise of offering an effective and less toxic treatment for tumours including medulloblastoma, the most common malignant brain tumour of childhood. Current treatment relies on the sensitivity of these tumours to DNA damage that was discovered more than 50 years ago. Finding new tumour-specific susceptibilities to complement sensitivity to DNA damage is key to developing new more effective adjuvant therapies. The specific metabolic program of tumours is an attractive vulnerability, as restriction diet are low cost and easy to implement. Here, we present compelling pre-clinical evidence that glutamine restriction diet can be used as an adjuvant treatment for p73-expressing medulloblastoma.
INSTITUTE
Queen Mary University of London
DEPARTMENT
Blizard Institute
LABORATORY
Centre for Genomics and Child Health
LAST_NAME
Marino
FIRST_NAME
Silvia
ADDRESS
4 Newark Street, E1 2AT, London
EMAIL
s.marino@qmul.ac.uk
PHONE
+44 20 7882 2360
NUM_GROUPS
2
TOTAL_SUBJECTS
18
STUDY_COMMENTS
We include 3 biological replicate with 3 technical replicates for each condition.
Alterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling
STUDY_SUMMARY
Non-invasive biomarkers are needed in inflammatory bowel disease (IBD) to help define disease activity and identify underlying pathogenic mechanisms. We hypothesized that serum metabolomics, which produces unique metabolite profiles, can aid in this search. The aim of this study was to characterize serum metabolomic profiles in patients with IBD, and to assess for differences between patients with ulcerative colitis (UC), Crohn disease (CD), and non-IBD subjects. Serum samples from 20 UC, 20 CD, and 20 non-IBD control subjects were obtained along with patient characteristics, including medication use and clinical disease activity. Non-targeted metabolomic profiling was performed using ultra-high performance liquid chromatography/mass spectrometry (UPLC-MS/MS) optimized for basic or acidic species and hydrophilic interaction liquid chromatography (HILIC/UPLC-MS/MS).
INSTITUTE
Vanderbilt University Medical Center
LAST_NAME
Elizabeth
FIRST_NAME
Scoville
ADDRESS
1030C MRB IV, 2215 Garland Avenue, Nashville, TN, 37232, USA
Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function
STUDY_SUMMARY
NAD(P)H-hydrate epimerase (EC 5.1.99.6) is known to help repair NAD(P)H hydrates (NAD(P)HX), which are damage products existing as R and S epimers. The S epimer is reconverted to NAD(P)H by a dehydratase; the epimerase facilitates epimer interconversion. Epimerase deficiency in humans causes a lethal disorder attributed to NADHX accumulation. However, bioinformatic evidence suggests caution about this attribution by predicting that the epimerase has a second function connected to vitamin B6 (pyridoxal 5'-phosphate and related compounds). Specifically, (i) the epimerase is fused to a B6 salvage enzyme in plants, (ii) epimerase genes cluster on the chromosome with B6-related genes in bacteria, and (iii) epimerase and B6-related genes are coexpressed in yeast and Arabidopsis. The predicted second function was explored in Escherichia coli, whose epimerase and dehydratase are fused and encoded by the yjeF gene. The putative NAD(P)HX epimerase active site has a conserved lysine residue (K192 in E. coli YjeF). Changing this residue to alanine cut in-vitro epimerase activity by ≥95% but did not affect dehydratase activity. Mutant cells carrying the K192A mutation had essentially normal NAD(P)HX levels, showing that the mutation had very little or no effect on NAD(P)HX repair in vivo. However, these cells showed metabolome changes, particularly in amino acids, that exceeded those in cells lacking the entire yjeF gene. The K192A mutant cells also had lower levels of free pyridoxal 5'-phosphate than wild-type cells. These results provide strong circumstantial evidence that the epimerase has a metabolic function beyond NAD(P)HX repair and that this function involves vitamin B6.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Pharmacometabolomic analysis of rat hippocampus and plasma in response to chronic stress and albiflorin treament
STUDY_TYPE
Animal study
STUDY_SUMMARY
Male Sprague-Dawley (SD) rats were exposed to one random stressor per day for 35 d. Following four weeks of stress exposure, rats with stress-induced depression-like behaviors were treated daily with either saline, fluoxetine or albiflorin for 7 days via intragastric gavage. Rat heparinized plasma was collected after drug treatment. After behavior tests, rats were sacrificed and the hippocampus was collected. Pharmacometabolomic analysis was conducted for both plasma and hippocampal samples
INSTITUTE
Beijing Woner Biotech Co. Ltd
LAST_NAME
Zhang
FIRST_NAME
Zuoguang
ADDRESS
No.9, Kexing Road, Fengtai, Beijing, Beijing, 101111, China
Metabolomics Linking Air Pollution, Obesity and Type 2 Diabetes
STUDY_TYPE
Untargeted high-resolution mass spectrometry profiling
STUDY_SUMMARY
The overall goal of this proposal is to use blood non-targeted high resolution metabolomics (HRM) to investigate the hypothesis that regional air pollution (NO2, PM2.5 and O3) and traffic-related air pollution exposures (traffic-related particulate matter components including EC2.5 and PM2.5 transition metals, and CALINE model-predicted NOx) alter key metabolic pathway(s) and that these alterations are associated with obesity and type 2 diabetes-related traits during the important developmental period of adolesence in the ongoing prospective Chidlren's Health study (CHS). Specific Aim 1 will examine the adverse impact of environmental chemicals in fasting blood samples measured by HRM on obesity (i.e., total body fat and body mass index (BMI)), metabolic dysfunction (e.g., fasting glucose and insulin concentrations and insulin resistance), and obesity-induced inflammation (i.e., leptin) among 104 Southern California adolescents enrolled in the CHS. Specific Aim 2 will examine associations of childhood exposures to PM2.5 and traffic-related air pollutants (i.e., CALINE model-predicted NOx) with biological metabolites identified in fasting blood samples using HRM among 104 adolescents in the CHS. Specific Aim 3 will investigate the metabolic pathways linking air pollution exposures and obesity and type 2 diabetes-related traits using pathway analysis under bayesian hierarchical model among 104 adolescents in the CHS.
INSTITUTE
Emory University School of Medicine
DEPARTMENT
Division of Pulmonary, Allergy and Critical Care Medicine
LABORATORY
Clincal Biomarkers Laboratory
LAST_NAME
Walker
FIRST_NAME
Douglas
ADDRESS
615 Michael St. Ste 225, Atlanta, GA, 30322, USA
EMAIL
douglas.walker@emory.edu
PHONE
(404) 727 5984
TOTAL_SUBJECTS
104
STUDY_COMMENTS
Both CHEAR and Clinical Biomarker Laboratory pooled plasma samples were used for quality control. Study specific sample pools were not created
Insights into the pathogenesis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) through metabolomic profiling of cerebrospinal fluid (part I)
STUDY_SUMMARY
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling illness characterized by six months or more of unexplained profound fatigue with post-exertional malaise, sleep abnormalities, cognitive dysfunction and autonomic disturbances. Focusing on the pathogenesis of central nervous system abnormalities in ME/CFS, we pursued metabolomics analysis of cerebrospinal fluid (CSF) in 32 ME/CFS cases, 40 subjects with multiple sclerosis (MS), another fatiguing illness, and 19 healthy subjects with no neurological disease (ND). MS/ND subjects were frequency matched for age and sex to ME/CFS subjects. Three untargeted metabolomic assays for primary metabolites, biogenic amines and complex lipids were performed with gas chromatography time-of-flight (GC-TOF) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) yielding profiles for 525 known metabolites. Mannose was a cardinal biomarker in ME/CFS subjects with reduced levels in ME/CFS compared to both MS and ND subjects. Levels of acetylcarnitine were reduced in ME/CFS vs. MS subjects. The predictive power of metabolomic analysis for diagnosis of ME/CFS vs. ND was higher (cross-validated AUC 0.875; 95% CI: 0.726~0.949) than with cytokine analysis alone (cross-validated AUC 0.865; 95% CI: 0.673~0.952) and improved with integration of both metabolomics and cytokine analyses (cross-validated AUC 0.916; 95% CI: 0.791~0.969). Our findings confirm the biological basis of ME/CFS, and may enable new methods for diagnosis and insight into cognitive and autonomic disturbances in this syndrome.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Insights into the pathogenesis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) through metabolomic profiling of cerebrospinal fluid (part II)
STUDY_SUMMARY
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling illness characterized by six months or more of unexplained profound fatigue with post-exertional malaise, sleep abnormalities, cognitive dysfunction and autonomic disturbances. Focusing on the pathogenesis of central nervous system abnormalities in ME/CFS, we pursued metabolomics analysis of cerebrospinal fluid (CSF) in 32 ME/CFS cases, 40 subjects with multiple sclerosis (MS), another fatiguing illness, and 19 healthy subjects with no neurological disease (ND). MS/ND subjects were frequency matched for age and sex to ME/CFS subjects. Three untargeted metabolomic assays for primary metabolites, biogenic amines and complex lipids were performed with gas chromatography time-of-flight (GC-TOF) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) yielding profiles for 525 known metabolites. Mannose was a cardinal biomarker in ME/CFS subjects with reduced levels in ME/CFS compared to both MS and ND subjects. Levels of acetylcarnitine were reduced in ME/CFS vs. MS subjects. The predictive power of metabolomic analysis for diagnosis of ME/CFS vs. ND was higher (cross-validated AUC 0.875; 95% CI: 0.726~0.949) than with cytokine analysis alone (cross-validated AUC 0.865; 95% CI: 0.673~0.952) and improved with integration of both metabolomics and cytokine analyses (cross-validated AUC 0.916; 95% CI: 0.791~0.969). Our findings confirm the biological basis of ME/CFS, and may enable new methods for diagnosis and insight into cognitive and autonomic disturbances in this syndrome.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Insights into the pathogenesis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) through metabolomic profiling of cerebrospinal fluid
STUDY_SUMMARY
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling illness characterized by six months or more of unexplained profound fatigue with post-exertional malaise, sleep abnormalities, cognitive dysfunction and autonomic disturbances. Focusing on the pathogenesis of central nervous system abnormalities in ME/CFS, we pursued metabolomics analysis of cerebrospinal fluid (CSF) in 32 ME/CFS cases, 40 subjects with multiple sclerosis (MS), another fatiguing illness, and 19 healthy subjects with no neurological disease (ND). MS/ND subjects were frequency matched for age and sex to ME/CFS subjects. Three untargeted metabolomic assays for primary metabolites, biogenic amines and complex lipids were performed with gas chromatography time-of-flight (GC-TOF) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) yielding profiles for 525 known metabolites. Mannose was a cardinal biomarker in ME/CFS subjects with reduced levels in ME/CFS compared to both MS and ND subjects. Levels of acetylcarnitine were reduced in ME/CFS vs. MS subjects. The predictive power of metabolomic analysis for diagnosis of ME/CFS vs. ND was higher (cross-validated AUC 0.875; 95% CI: 0.726~0.949) than with cytokine analysis alone (cross-validated AUC 0.865; 95% CI: 0.673~0.952) and improved with integration of both metabolomics and cytokine analyses (cross-validated AUC 0.916; 95% CI: 0.791~0.969). Our findings confirm the biological basis of ME/CFS, and may enable new methods for diagnosis and insight into cognitive and autonomic disturbances in this syndrome.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Insights into the pathogenesis of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) through metabolomic profiling of cerebrospinal fluid
STUDY_SUMMARY
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disabling illness characterized by six months or more of unexplained profound fatigue with post-exertional malaise, sleep abnormalities, cognitive dysfunction and autonomic disturbances. Focusing on the pathogenesis of central nervous system abnormalities in ME/CFS, we pursued metabolomics analysis of cerebrospinal fluid (CSF) in 32 ME/CFS cases, 40 subjects with multiple sclerosis (MS), another fatiguing illness, and 19 healthy subjects with no neurological disease (ND). MS/ND subjects were frequency matched for age and sex to ME/CFS subjects. Three untargeted metabolomic assays for primary metabolites, biogenic amines and complex lipids were performed with gas chromatography time-of-flight (GC-TOF) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) yielding profiles for 525 known metabolites. Mannose was a cardinal biomarker in ME/CFS subjects with reduced levels in ME/CFS compared to both MS and ND subjects. Levels of acetylcarnitine were reduced in ME/CFS vs. MS subjects. The predictive power of metabolomic analysis for diagnosis of ME/CFS vs. ND was higher (cross-validated AUC 0.875; 95% CI: 0.726~0.949) than with cytokine analysis alone (cross-validated AUC 0.865; 95% CI: 0.673~0.952) and improved with integration of both metabolomics and cytokine analyses (cross-validated AUC 0.916; 95% CI: 0.791~0.969). Our findings confirm the biological basis of ME/CFS, and may enable new methods for diagnosis and insight into cognitive and autonomic disturbances in this syndrome.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. Part 1:Liver
STUDY_TYPE
Lipidomics Study
STUDY_SUMMARY
The spectrum of nonalcoholic fatty liver disease (NAFLD) includes steatosis, nonalcoholic steatohepatitis (NASH), and cirrhosis. Recognition and timely diagnosis of these different stages, particularly NASH, is important for both potential reversibility and limitation of complications. Liver biopsy remains the clinical standard for definitive diagnosis. Diagnostic tools minimizing the need for invasive procedures or that add information to histologic data are important in novel management strategies for the growing epidemic of NAFLD. We describe an 'omics' approach to detecting a reproducible signature of lipid metabolites, aqueous intracellular metabolites, SNPs, and mRNA transcripts in a double-blinded study of patients with different stages of NAFLD that involves profiling liver biopsies, plasma, and urine samples. Using linear discriminant analysis, a panel of 20 plasma metabolites that includes glycerophospholipids, sphingolipids, sterols, and various aqueous small molecular weight components involved in cellular metabolic pathways, can be used to differentiate between NASH and steatosis. This identification of differential biomolecular signatures has the potential to improve clinical diagnosis and facilitate therapeutic intervention of NAFLD.
Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. Part 1:Plasma
STUDY_TYPE
Lipidomics Study
STUDY_SUMMARY
The spectrum of nonalcoholic fatty liver disease (NAFLD) includes steatosis, nonalcoholic steatohepatitis (NASH), and cirrhosis. Recognition and timely diagnosis of these different stages, particularly NASH, is important for both potential reversibility and limitation of complications. Liver biopsy remains the clinical standard for definitive diagnosis. Diagnostic tools minimizing the need for invasive procedures or that add information to histologic data are important in novel management strategies for the growing epidemic of NAFLD. We describe an 'omics' approach to detecting a reproducible signature of lipid metabolites, aqueous intracellular metabolites, SNPs, and mRNA transcripts in a double-blinded study of patients with different stages of NAFLD that involves profiling liver biopsies, plasma, and urine samples. Using linear discriminant analysis, a panel of 20 plasma metabolites that includes glycerophospholipids, sphingolipids, sterols, and various aqueous small molecular weight components involved in cellular metabolic pathways, can be used to differentiate between NASH and steatosis. This identification of differential biomolecular signatures has the potential to improve clinical diagnosis and facilitate therapeutic intervention of NAFLD.
Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. Part 3:Urine
STUDY_TYPE
Lipidomics Study
STUDY_SUMMARY
The spectrum of nonalcoholic fatty liver disease (NAFLD) includes steatosis, nonalcoholic steatohepatitis (NASH), and cirrhosis. Recognition and timely diagnosis of these different stages, particularly NASH, is important for both potential reversibility and limitation of complications. Liver biopsy remains the clinical standard for definitive diagnosis. Diagnostic tools minimizing the need for invasive procedures or that add information to histologic data are important in novel management strategies for the growing epidemic of NAFLD. We describe an 'omics' approach to detecting a reproducible signature of lipid metabolites, aqueous intracellular metabolites, SNPs, and mRNA transcripts in a double-blinded study of patients with different stages of NAFLD that involves profiling liver biopsies, plasma, and urine samples. Using linear discriminant analysis, a panel of 20 plasma metabolites that includes glycerophospholipids, sphingolipids, sterols, and various aqueous small molecular weight components involved in cellular metabolic pathways, can be used to differentiate between NASH and steatosis. This identification of differential biomolecular signatures has the potential to improve clinical diagnosis and facilitate therapeutic intervention of NAFLD.
Breast cancer is a highly heterogeneous disease associated with metabolic reprogramming. The shifts in the metabolome caused by breast cancer still lack data from Latin populations of Hispanic origin. In this pilot study, metabolomic and lipidomic approaches were performed to establish a plasma metabolic fingerprint of Colombian Hispanic women with breast cancer. NMR, GC-MS and LC-MS datasets were combined and compared. Statistics showed discrimination between breast cancer and healthy subjects on all analytical platforms.
Discovery of Lipidome Alterations Following Traumatic Brain Injury via High-Resolution Metabolomics
STUDY_TYPE
Untargeted lipidomics
STUDY_SUMMARY
Traumatic brain injury (TBI) can occur across wide segments of the population, presenting in a heterogeneous manner that makes diagnosis inconsistent and management challenging. Biomarkers offer the potential to objectively identify injury status, severity, and phenotype by measuring the relative concentrations of endogenous molecules in readily accessible biofluids. Through a data-driven, discovery approach, novel biomarker candidates for TBI were identified in the serum lipidome of adult male Sprague-Dawley rats in the first week following moderate controlled cortical impact (CCI). Serum samples were analyzed in positive and negative ion modes by Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS). A predictive panel for the classification of injured and uninjured sera samples, consisting of 26 dysregulated species belonging to a variety of lipid classes, was developed with a cross-validated accuracy of 85.3% using omniClassifier software to optimize feature selection,. Polyunsaturated fatty acids (PUFAs) and PUFA-containing diacylglycerols were found to be upregulated in sera from injured rats, while changes in sphingolipids and other membrane phospholipids were also observed, many of which map to known secondary injury pathways. Overall, the identified biomarker panel offers viable molecular candidates representing lipids that may readily cross the blood brain barrier (BBB) and aid in the understanding of TBI pathophysiology.
Karenia brevis allelopathy compromises the lipidome, membrane integrity, and photosynthetic efficiency of competitors
STUDY_TYPE
Untargeted lipidomics
STUDY_SUMMARY
Allelopathy, or the release of compounds that inhibit competitors, is a form of interference competition that is common among bloom-forming phytoplankton. Allelopathy is hypothesized to play a role in bloom propagation and maintenance and is well established in the red tide dinoflagellate Karenia brevis. K. brevis typically suppresses competitor growth through unknown mechanisms over the course of many days. When we investigated the effects of allelopathy on the lipidomes of two competing phytoplankton, Asterionellopsis glacialis and Thalassiosira pseudonana using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS)- based metabolomics, we found that the lipidomes of both species were significantly altered, however A. glacialis maintained a more robust response whereas T. pseudonana saw significant alterations in fatty acid synthesis, cell membrane integrity, and a decrease in photosynthetic efficiency. Membrane- associated lipids were significantly suppressed for T. pseudonana exposed to allelopathy to the point of permeabilizing the cell membrane of living cells. The dominant mechanisms of K. brevis allelopathy appear to target lipid biosynthesis affecting multiple physiological pathways suggesting that exuded compounds have the ability to significantly alter competitor physiology and give K. brevis a competitive edge over sensitive species.
Longitudinal Metabolomics of the Human Microbiome in Inflammatory Bowel Disease
STUDY_SUMMARY
A number of factors contribute to the complex array of small molecules that occur in stool; including diet, gut flora, and gut function. Comprehensive profiling of the stool metabolome therefore can provide detailed phenotypic information on health status, metabolic interactions between the host and the microbiome, and interactions among gut microbes. Here, we applied metabolomics to characterize stool samples collected longitudinally from inflammatory bowel disease (IBD) patients and non-IBD controls who participated in the Integrative Human Microbiome Project (iHMP). A total of 546 stool samples were analyzed using a platform comprised of four complementary liquid chromatography tandem mass spectrometry (LC-MS) methods designed to measure polar metabolites and lipids. Each method used high resolution/accurate mass (HRAM) profiling to measure both metabolites of confirmed identity and yet to be identified metabolite peaks. 81,867 de-isotoped LC-MS peaks were measured, out of which 597 were annotated based on confirmation with authentic reference standards. Pooled stool extracts inserted and analyzed throughout the analysis queues to evaluate analytical reproducibility showed a median coefficient of variation of 5.1% among known metabolites and 24.2% across all 81,867 features. Owing to differences in water content and heterogeneity among stool samples, total median scaling was used to standardize the metabolomics data. In addition to being accessible at the Metabolomics Workbench repository, these metabolomics data will be incorporated into a multi’omic database (https://www.hmpdacc.org/ihmp/) that will enable the study of associations between the gut microbiome and IBD.
MuRF1-Related Metabolic Alterations in HL-1 Cardiomyocyte Induced by Cyclic Stretch
STUDY_TYPE
Cardiomyocyte cell culture
STUDY_SUMMARY
We collected cell media and performed GC-MS non-targeted metabolomics to identify the role of MuRF1 in the dynamic metabolic changes in cardiomyocytes.
MuRF1-Related Metabolomic Changes in Stretched and Unloaded HL-1 Cells
STUDY_SUMMARY
Introduction: Left ventricular assist devices (LVADs) provide significant pressure and volume unloading, which reverse key structural features of heart failure, including hypertrophy, fibrosis, and altered sympathetic innervation. This has led to LVADs increasing utilization as both a bridge or destination therapy for heart failure. While distinct metabolic changes occur in the human myocardium with LVAD placement, the specific molecular mechanisms underlying these changes have not been identified. Objectives: To identify the role of MuRF1 in the metabolic changes in cardiomyocytes unloading in vitro. Methods: HL-1 atrial cardiomyocyte cells were plated on silastic membranes coated with gelatin/fibronectin and transduced with AdshRNA MuRF1 (or AdshRNA Scramble control) to knock-down MuRF1 protein to <25% of controls and subjected to 15% biaxial stretch at 1 Hz using the Flexcell FX-5000™ Compression System in serum free DMEM (or no-stretch). After 6 hours stretch, media was collected in parallel with time-matched no-stretch controls, followed by serial collections at 1, 3, 6, and 12 hours unloading (i.e. after termination of stretch). Media was analyzed by untargeted metabolomics using GC-MS. Results: After 6 hours stretch, control HL-1 cell media (AdshRNA Scramble) had 19 significantly altered metabolites compared to non-stretched control cell media (AdshRNA Scramble) by t-test, involved in: 1) glyoxylate and dicarboxylate metabolism (p=0.00087043, FDR=0.071375), 2) methane metabolism (p=0.0041113, FDR=0.089824), 3) glycine, serine and threonine metabolism (p=0.0043816, FDR=0.089824), and 4) aminoacyl-tRNA biosynthesis(p=0.0060141, FDR=0.09863). To determine the role of MuRF1 in stretch, we additionally compared the AdshRNA Scramble groups to AdshRNA MuRF1 +/- stretch at 6 hours and identified 41 significant metabolites (of 79 identified) by ANOVA, involved in: 1) phenylalanine, tyrosine, and tryptophan biosynthesis (p=0.0036482, FDR=0.05983), 2) aminoacyl-tRNA biosynthesis (p=3.74E-07, FDR=3.06E-05), and 3) valine, leucine, and isoleucine biosynthesis (p=0.0021624, FDR=0.053255). We next compared the 6 hour stretch time point of the four groups to the 1, 3, 6, and 12 hours unloading conditions to identify MuRF1-associated metabolites during the unloading period. At 12 hours of unloading (representative 1, 3, and 6 hours unloading), MuRF1 knock-down cell media had 35 (of 82 named metabolites) significantly different metabolites by ANOVA involved in 1) phenylalanine, tyrosine and tryptophan biosynthesis (p=0.0023668, FDR=0.048519), 2) aminoacyl-tRNA biosynthesis (p=0.0011403, FDR=0.0032631), 3) phenylalanine metabolism (P= 0.0011403, FDR 0.042673),and arginine and proline metabolism (p=0.0015612, FDR 0.042673). A final analysis comparing all four groups across all five time points identified 21 significant metabolites. When MuRF1 was knocked down (no stretch), these 21 metabolites were significantly increased without stretch. In response to stretch and unloading, these metabolites were further decreased in AdshRNA Scramble (control) cell media decreased. In contrast, these stretch and unloading induced decreases were attenuated in AdshRNA MuRF1 cell media. These metabolites included nine (9) amino acids (citrulline, phenylalanine, tyrosine, asparagine, 2-ketovaline, and -ketoleucine/ketoisoleucine, threonine, isoleucine, leucine), three (3) metabolic co-factors (Pantothenic acid, Myoinositol, 5,6-Dihydrouracil), and one fatty acid (stearic acid). Conclusion: These studies identify for the first time a role for MuRF1 in generating key amino acids recently reported in LVAD unloading in human myocardium using an in vitro model of atrial cardiomyocyte unloading.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm road, Chapel Hill, North Carolina, 27599-7126, USA
Metabolomics Analysis of Aqueous Humour in the Presence of Glaucoma Drainage Devices
STUDY_TYPE
Metabolomics Evaluation of Aqueous Humor Samples from Left (treated) and Right (Control) Eyes of Rabbits.
STUDY_SUMMARY
Metabolomic experiments were carried out on aqueous humor samples provided by Ramesh Ayyala. Through this collaboration, we propose to study aqueous humor from control and experimental rabbits to better understand metabolic differences in the aqueous humor samples.
Define alterations in the gut metabolome of mice infected with C. difficile
STUDY_TYPE
Time course experiment
STUDY_SUMMARY
C57BL/6 mice were treated with antibiotics to make them susceptible to C. difficile. Mice were challenged with C. difficile and the infection was monitored for 30 hours post challenge. Mice were sacrificed at 0 hr, 12 hr, 24 hr, and 30 hr post challenge with C. difficile and gut content was collected for untargeted metabolomic analysis. The aim of this project was to define the gut metabolome throughout C. difficile infection.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3915 (CwlM)
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv0100
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Metabolome profiles in urogenital schistosomiasis and associated pathologies
STUDY_SUMMARY
Metabolic fingerprint aid discovery of new biomarkers. Blood and urine were collected from volunteers in Eggua community, Nigeria, after ethical approval. LC-ESI-MS were used to analyse samples. Bioinformatics and statistical tools were used to detect important metabolites
INSTITUTE
University of Ibadan, Nigeria
DEPARTMENT
Zoology (Cell biology and Genetics unit)
LABORATORY
Centre for Materials Characterization, National Chemical Laboratory, Pune, India
LAST_NAME
Adebayo
FIRST_NAME
Adewale
ADDRESS
Cell Biology and Genetics unit, Department of zoology, University of ibadan, Nigeria/ National Centre for Cell Science, Pune, India
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv2553c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv2247
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3208
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Utilizing Ion Mobility Spectrometry and Mass Spectrometry for the Analysis of Polycyclic Aromatic Hydrocarbons, Polychlorinated Biphenyls, Polybrominated Diphenyl Ethers and Their Metabolites mass spectrometry
STUDY_TYPE
Structural analysis of xenobiotics using ion mobility
STUDY_SUMMARY
Standards of xenobiotics were analyzed with Agilent 6560 Ion mobility QTOF MS platform to find Collision Cross Section values. All measurements were performed in triplicate in both positive and negative polarities with nitrogen gas and at seven different electric fields, so that values could be directly measured and random standard deviations (RSD) assessed for each molecule.
INSTITUTE
Pacific Northwest National Laboratory
DEPARTMENT
Integrative Omics
LABORATORY
Pacific Northwest National Laboratory
LAST_NAME
Baker
FIRST_NAME
Erin
ADDRESS
Pacific Northwest National Laboratory 902 Battelle Boulevard Richland, WA
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3285
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3651
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3799c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3916c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Specific Aims: (a) Identify sex differences in serum untargeted metabolomics profiles during late adolescence, (b) examine changes in metabolomics profiles between early and late adolescence in the same children, and (c) evaluate associations of exposure to prenatal and concurrent exposure to PAHs, metals, and EDCs with serum metabolite profiles among boys and girls, separately, during late adolescence.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
EMAIL
mkachman@med.umich.edu
PHONE
(734) 232-8175
NUM_GROUPS
2
TOTAL_SUBJECTS
207
STUDY_COMMENTS
The overall objective of this project is to expand upon available data from Early Life Exposure in Mexico to ENvironental Toxicants (ELEMENT) Project to examine effects of toxicant exposures during three sensitive developmental timeframes – the prenatal period, early adolescence, and late adolescence – on adiposity and metabolic risk in adolescence with an emphasis on sex differences and the related molecular underpinnings. In addition to existing exposure data on BPA, metals and phthalates, we propose to add measures of polycyclic aromatic hydrocarbon (PAH) metabolites in archived urine samples from mothers and children. We also propose to assess the epigenome at three developmental periods (prenatal aka in utero, early and late adolescence) and the circulating metabolome during late adolescence. We will incorporate data on toxicant exposures and ‘omics, including untargeted metabolomics of 404 teenagers from the ELEMENT cohorts, to addressing several specific aims.
Mechanisms for Insulin Resistance in Polycystic Ovary Syndrome: aminoadipic acid, lysine concentrations, and enrichment (part I)
STUDY_SUMMARY
To determine whether altered lysine and α-aminoadipic acid (AAA) kinetics explain previous observations of increased lysine and AAA concentrations in PCOS compared to controls, as measured by baseline lysine and AAA flux in PCOS versus healthy controls using [α-15N]-lysine and [13C]-AAA stable isotope tracers as well as by comparing the conversion of [α-15N]-lysine to [15N]-AAA. To evaluate how hyperinsulinemia affects lysine and AAA kinetics. Changes in lysine and AAA flux during a hyperinsulinemic-euglycemic clamp will be evaluated in healthy controls and compared to the baseline changes in lysine and AAA flux in PCOS.
INSTITUTE
Mayo Clinic
LAST_NAME
Chang
FIRST_NAME
Al
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Mechanisms for Insulin Resistance in Polycystic Ovary Syndrome: aminoadipic acid, lysine concentrations, and enrichment (part II)
STUDY_SUMMARY
To determine how metformin therapy changes lysine and AAA kinetics in PCOS and whether this is associated with improvements in insulin sensitivity. Changes in lysine and AAA flux before and after three months of metformin therapy will be compared to women with PCOS randomized to no treatment for three months.
INSTITUTE
Mayo Clinic
LAST_NAME
Chang
FIRST_NAME
Alice
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Using Metabolomics and Lipidomics Analysis to Explore Metabolites and Pathways Associated Increased Airway Hyperresponsiveness in Patients with Asthma who are Identified by Race (African American) and Genotype (ADRB2 Arg16/Arg)
STUDY_TYPE
Open-label, prospective cohort study
STUDY_SUMMARY
Asthma is a heterogeneous disease largely defined by chronic airway inflammation with similar symptomatology in patients that includes wheezing, shortness of breath, chest tightness and cough. However, underlying these common symptoms are varying endotypes with distinct pathophysiological processes. Metabolomic studies in patients with asthma are emerging and suggest that metabolomics can characterize distinct asthma phenotypes. In a completed study, we identified a population of patients with asthma who have increased airway hyperresponsiveness (airway hyperresponsiveness is a marker for asthma disease severity) who are characterized by race (African American) and genotype (ADRB2 Arg16/Arg) compared with patients who have less airway hyperresponsiveness (African Americans and whites with differing ADRB2 genotypes). This group may represent a distinct endotype of asthma with unique metabolomic and lipidomic characteristics. The aims of this project are to (1) use metabolomic and lipidomic analysis to identify metabolites present in plasma in this population of patients with asthma who have increased airway hyperresponsiveness (African Americans who carry the ADRB2 Arg16/Arg genotype) and patients with asthma who have less airway hyperresponsiveness (African Americans and whites with differing ADRB2 genotypes); and (2) identify pathways that will improve the understanding of increased airway hyperresponsiveness in this population. We hypothesize that there will be unique metabolic pathways in the population with increased airway hyperresponsiveness that will be distinct from pathways in patients with lower airway hyperresponsiveness. In this project will use data and samples that were previously collected as part of the NIH funded project “Pharmacogenetics of β2-Agonists in Asthma” (Blake, PI K23 HL081245). Blood was collected in 55 African Americans and whites after receiving 2-weeks treatment with inhaled fluticasone. Samples were stored on ice until processed and plasma frozen at -80°C. If our findings indicate distinct metabolic pathways are present using global metabolomic and lipodomic analysis, we will seek to replicate our findings using samples and data from phenotypically well characterized participants who participated in trials conducted through the American Lung Association Airways Clinical Research Centers network, of which Nemours has been a highly productive site since 1999. Future controlled trials would be conducted to evaluate treatments based upon molecular pathways identified through metabolomic and lipidomic analysis.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Beecher
FIRST_NAME
Chris
ADDRESS
PO Box 100219 Gainesville FL 32610-0219 , Southeast Center for Integrated Metabolomics
EMAIL
chris@iroatech.com
PHONE
(352) 294-4385
NUM_GROUPS
4
TOTAL_SUBJECTS
55
STUDY_COMMENTS
Nubmer of groups : 4 (race x diplotype); SECIM pilot and feasibility, NIH U24 DK097209
Isolated T cells were activated for 48-72 hours in the presence and absence of 5mM DFMO, an ODC inhibitor
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Hesterberg
FIRST_NAME
Rebecca
ADDRESS
12902 Magnolia Dr
EMAIL
rebecca.hesterberg@moffitt.org
PHONE
813-270-9181
NUM_GROUPS
4
TOTAL_SUBJECTS
16
STUDY_COMMENTS
OT-1 mice express a transgenic T cell receptor in all CD8+ T cells that binds with high affinity to a peptide derived from the protein ovalbumin (SIINFEKL).
Determine metabolomics signatures important for the ability of Streptococus gallolyticus to promote colon cancer cell proliferation
STUDY_SUMMARY
HT29 cells were treated with Sg TX20005 stationary phase, Sg TX20005 exponential phase (negative control), and Sg TX20008 stationary phase (negative control), and media only (baseline control). The cells were washed and aliquoted. One aliquot was pelleted and stored at -80C for metabolomics analysis. DNA was also extracted from the other aliquot for DNA methylation studies.
Pediatric obesity has more than doubled in children and tripled in adolescents over the past 30 years. Recent findings demonstrate that differences in energy harvesting bacteria promote obesity in the host and appear to be influenced by early life factors such as mode of delivery, maternal obesity, and breastfeeding. The goal of this proposal is to investigate how human milk impacts the infant gut microbiome during the first 12-months of life and identify the microbe-host interactions that mediates the protective role of breastfeeding on infant adiposity. The results of this exploratory study will characterize factors that influence microbial transmission between mothers and offspring and identify human milk compounds that stabilize a healthy infant microbiome with potential to reduce pediatric obesity.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LABORATORY
R1-187
LAST_NAME
Carney
FIRST_NAME
Olivia
ADDRESS
Clinical and Translational Research Building, University of Florida College of Medicine, 2004 Mowry Road, Gainesville, FL 32608
EMAIL
ocarney1@ufl.edu
PHONE
352-294-8361
NUM_GROUPS
3
TOTAL_SUBJECTS
12
STUDY_COMMENTS
12 samples (4 mothers with 3 human milk fractions: fat, skim and whole)
The Influence of Sugar, Artificial Sweeteners, and the Microbiome on Rodent TCA Concentrations (part I)
STUDY_SUMMARY
Targeted TCA concentrations of rodents treated with diets rich in commonly used artifically sweeteners will be assessed in this study. We hypothesized that a specific subset of plasma metabolites are generated as a result from a diet rich in commonly used artificial sweeteners and their subsequent processing by the gut microbiome, which could ultimately lead to impaired glycemic control and negative physiological health outcomes. To test this hypothesis we administered normal, high glucose, fructose, aspartame, and acesulfame potassium diets to rats for 3 weeks, followed by a plasma collection through cardiac puncture and metabolic analysis. We also treated the gut microbiota with in rats with the same diets plus bacitracin/streptomycin to observe how alterations of the microbiome influence the plasma metabolic profile in these animals. The resulting data will give us insights into the influence of high sugar and artificial sweetener diets on homeostatic metabolic processes and dive into the symbiotic relationship of the gut microbiome with this process.
The Influence of Sugar, Artificial Sweeteners, and the Microbiome on Rodent Diacylglycerols (part II)
STUDY_SUMMARY
Targeted diacylglycerols panel of rodents treated with diets rich in commonly used artifically sweeteners will be assessed in this study. We hypothesized that a specific subset of plasma metabolites are generated as a result from a diet rich in commonly used artificial sweeteners and their subsequent processing by the gut microbiome, which could ultimately lead to impaired glycemic control and negative physiological health outcomes. To test this hypothesis we administered normal, high glucose, fructose, aspartame, and acesulfame potassium diets to rats for 3 weeks, followed by a plasma collection through cardiac puncture and metabolic analysis. We also treated the gut microbiota with in rats with the same diets plus bacitracin/streptomycin to observe how alterations of the microbiome influence the plasma metabolic profile in these animals. The resulting data will give us insights into the influence of high sugar and artificial sweetener diets on homeostatic metabolic processes and dive into the symbiotic relationship of the gut microbiome with this process.
The Influence of Sugar, Artificial Sweeteners, and the Microbiome on Rodent Triglyceride Composition (part III)
STUDY_SUMMARY
Targeted triglyceride concentration panel of rodents treated with diets rich in commonly used artifically sweeteners will be assessed in this study. We hypothesized that a specific subset of plasma metabolites are generated as a result from a diet rich in commonly used artificial sweeteners and their subsequent processing by the gut microbiome, which could ultimately lead to impaired glycemic control and negative physiological health outcomes. To test this hypothesis we administered normal, high glucose, fructose, aspartame, and acesulfame potassium diets to rats for 3 weeks, followed by a plasma collection through cardiac puncture and metabolic analysis. We also treated the gut microbiota with in rats with the same diets plus bacitracin/streptomycin to observe how alterations of the microbiome influence the plasma metabolic profile in these animals. The resulting data will give us insights into the influence of high sugar and artificial sweetener diets on homeostatic metabolic processes and dive into the symbiotic relationship of the gut microbiome with this process.
The Influence of Sugar, Artificial Sweeteners, and the Microbiome on Rodent Amino Acids (part IV)
STUDY_SUMMARY
Targeted Amino Acid panel of rodents treated with diets rich in commonly used artifically sweeteners will be assessed in this study. We hypothesized that a specific subset of plasma metabolites are generated as a result from a diet rich in commonly used artificial sweeteners and their subsequent processing by the gut microbiome, which could ultimately lead to impaired glycemic control and negative physiological health outcomes. To test this hypothesis we administered normal, high glucose, fructose, aspartame, and acesulfame potassium diets to rats for 3 weeks, followed by a plasma collection through cardiac puncture and metabolic analysis. We also treated the gut microbiota with in rats with the same diets plus bacitracin/streptomycin to observe how alterations of the microbiome influence the plasma metabolic profile in these animals. The resulting data will give us insights into the influence of high sugar and artificial sweetener diets on homeostatic metabolic processes and dive into the symbiotic relationship of the gut microbiome with this process.
Lipidomics of inflammation-induced optic nerve regeneration
STUDY_TYPE
untargeted LC-MS/MS profiling
STUDY_SUMMARY
In adult mammals, retinal ganglion cells (RGCs) fail to regenerate their axons when damaged. As a result, RGCs die after acute injury and in progressive degenerative diseases such as glaucoma; such damage can lead to permanent vision loss and blindness. Little is known about the roles of lipids in axon injury and repair despite their fundamental importance in composition of cell membranes, myelin sheaths and mediation of signaling pathways. Study of the lipidome in the biology of optic nerve (ON) regeneration has been largely neglected. A better understanding of the roles that lipids play in RGC biology may enhance understanding of RGC-related diseases and point to novel treatments. Established experimental models of ON regeneration allow exploration of molecular determinants of RGC axon regenerative success and failure. In this study, we used high-resolution liquid chromatography-tandem mass spectrometry to analyze lipidomic profiles of the ON and retina in an ON crush model with and without intravitreal Zymosan injections to enhance regeneration. Our results reveal profound remodeling of retina and ON lipidomes that occur after injury. In the retina, Zymosan treatment largely abrogates widespread lipidome alterations. In the ON, Zymosan induces lipid profiles that are distinct from those observed in naïve and vehicle-injected crush controls. We have identified a number of lipid species, classes and fatty acids that may be involved in the mechanisms of axon damage and repair. Lipids upregulated during RGC regeneration may be interesting candidates for further functional studies.
U13C Glucose Tracing of Young and Old Pancreatic Islets
STUDY_SUMMARY
Pancreatic islets from young and old mice were traced with either 2.8mM or 16.8mM U13C glucose to determine the effect of age upon glucose metabolism in basal and stimulated states.
Timecourse of U13C glucose labeling of pancreatic islets in young mice
STUDY_SUMMARY
Pancreatic islets from young mice were traced with 16.8mM U13C glucose over a 90 minute timecourse to determine the rate of metabolite labeling during glucose stimulation.
Metabolite and gene expression profiles suggest a putative mechanism through which high dietary carbohydrates reduce the content of hepatic betaine in Megalobrama amblycephala
STUDY_SUMMARY
plasma of Megalobrama amblycephala fed with control diet, high carbohydrates diet,betaine diet with 16 weeks and betaine diet with 4 weeks.
INSTITUTE
College of Fisheries Huazhong Agricultural University
Impact of thiamine metabolites and spent medium from Chlorella sorokiniana on metabolism in the green algae Auxenochlorella prototheciodes (part I)
STUDY_SUMMARY
The purpose of this study is to determine how thiamine metabolites impact central metabolism in Auxenochlorella protothecoides when grown in the presence of glucose. We hypothesize that thiamine metabolites alleviate bottlenecks in the TCA cycle and gluconeogensis, thus allowing for greater starch production when they are present. Cells were grown in bioreactors: 3 control cultures with no thiamine metabolites, 3 cultures received thiamine, 3 recieved HMP, and 3 were grown on residual medium from another algae species - Chlorella sorokiniana. We suspect that this residual medium also contains thiamine metabolites. Samples were taken daily from each of these 12 cultures over a 5 day time course so that we can observe build-up of metabolites over time.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Impact of thiamine metabolites and spent medium from Chlorella sorokiniana on metabolism in the green algae Auxenochlorella prototheciodes (part II)
STUDY_SUMMARY
The purpose of this study is to determine how thiamine metabolites impact central metabolism in Auxenochlorella protothecoides when grown in the presence of glucose. We hypothesize that thiamine metabolites alleviate bottlenecks in the TCA cycle and gluconeogensis, thus allowing for greater starch production when they are present. Cells were grown in bioreactors: 3 control cultures with no thiamine metabolites, 3 cultures received thiamine, 3 recieved HMP, and 3 were grown on residual medium from another algae species - Chlorella sorokiniana. We suspect that this residual medium also contains thiamine metabolites. Samples were taken daily from each of these 12 cultures over a 5 day time course so that we can observe build-up of metabolites over time.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
The Influence of Sugar, Artificial Sweeteners, and the Microbiome on Rodent Large Scale Profiling (part V)
STUDY_SUMMARY
Large scale profiling of rodents treated with diets rich in commonly used artifically sweeteners will be assessed in this study. We hypothesized that a specific subset of plasma metabolites are generated as a result from a diet rich in commonly used artificial sweeteners and their subsequent processing by the gut microbiome, which could ultimately lead to impaired glycemic control and negative physiological health outcomes. To test this hypothesis we administered normal, high glucose, fructose, aspartame, and acesulfame potassium diets to rats for 3 weeks, followed by a plasma collection through cardiac puncture and metabolic analysis. We also treated the gut microbiota with in rats with the same diets plus bacitracin/streptomycin to observe how alterations of the microbiome influence the plasma metabolic profile in these animals. The resulting data will give us insights into the influence of high sugar and artificial sweetener diets on homeostatic metabolic processes and dive into the symbiotic relationship of the gut microbiome with this process.
High Resolution GC-MS Metabolomics of Non-Human Primate Serum
STUDY_TYPE
Non-human Primate Serum
STUDY_SUMMARY
Rationale: Metabolomics analyses using gas chromatography mass spectrometry (GC-MS) - based metabolomics are heavily impeded by the lack of high-resolution mass spectrometers and limited spectral libraries to complement the excellent chromatography that GC platforms offer, a challenge that is being addressed with the implementation of high resolution (HR) platforms such as GC-Orbitrap-MS. Methods: We used serum samples from a non-human primate (NHP), a baboon (Papio hamadryas), with suitable quality controls to quantify the chemical space using an advanced HR MS platform for confident metabolite identification and robust quantification to assess the suitability of the platform for routine clinical metabolomics research. In a comparative approach, we also analyzed the same serum samples using a two-dimensional gas chromatography time-of-flight mass-spectrometer (2D GC-ToF-MS) for metabolite identification and quantification following established standard protocols. Results: Overall, the 2D GC-ToF-MS and GC-Orbitrap-MS analyses enabled identification and quantification of 555 total metabolites from the NHP serum with a spectral similarity score Rsim ≥ 900 and S/R ratio of > 25. A common set of 30 metabolites with HMDB and KEGG IDs were quantified in the serum samples by both platforms where the 2D GC-ToF-MS enabled quantification of a total 384 metabolites (118 HMDB IDs) and the GC-Orbitrap-MS analysis quantification of a total 200 metabolites (47 HMDB IDs). Conclusions: Our study provides insights into the benefits and limitations of the use of a higher mass accuracy instrument for untargeted GC-MS-based metabolomics with multi-dimensional chromatography in future studies addressing clinical conditions or exposome studies.
Metabolome profiles in urogenital schistosomiasis and associated pathologies (part II)
STUDY_SUMMARY
Metabolic fingerprint aid discovery of new biomarkers. Blood and urine were collected from volunteers in Eggua community, Nigeria, after ethical approval. LC-ESI-MS were used to analyse samples. Bioinformatics and statistical tools were used to detect important metabolites
INSTITUTE
University of Ibadan, Nigeria
DEPARTMENT
Zoology (Cell biology and Genetics unit)
LABORATORY
Centre for Materials Characterization, National Chemical Laboratory, Pune, India
LAST_NAME
Adebayo
FIRST_NAME
Adewale
ADDRESS
Cell Biology and Genetics unit, Department of zoology, University of ibadan, Nigeria/ National Centre for Cell Science, Pune, India
Metabolomic analysis of TB vs heathy including time to TB.
STUDY_SUMMARY
Within the GC6-74 cohorts, 4,462 HIV-negative healthy household contacts of 1,098 index TB cases were recruited from 2006 to 2012 at four African sites included in this study i.e. SUN (Stellenbosch University, South Africa), MRC (Medical Research Council Unit, The Gambia), AHRI (Armauer Hansen Research Institute, Ethiopia) and MAK (Makerere University, Uganda). The study had an exclusion period of 3 months, such that participants, who were diagnosed with active TB within 3 months of enrolment, were excluded from analysis to prevent inclusion of participants who had incipient or asymptomatic clinical TB disease at enrolment. Additional exclusion criteria were positive HIV rapid test, current or previous anti-retroviral treatment, history of TB, pregnancy, participation in drug and/or vaccine clinical trials and chronic disease diagnosis or immunosuppressive therapy within the past 6 months, and living in the study area for less than 3 months. A total of 97 individuals who developed active TB within the two year follow-up period were included in this study and matched at a ratio of 1:4 with participants who remained healthy during the 2-year follow-up period (controls); matching, by site, age class, sex, and wherever possible year of recruitment. Initial samples collected upon enrolment were termed baseline (BL) samples. Further samples were taken 6 and 18 months post-exposure, provided that the participant had remained TB free at the time of sample collection. Metabolic profiling was carried out for each study site, using either serum or plasma samples. For a small number of samples, an insufficient amount of plasma was available, so the sample was diluted using RPMI buffer.
GC6-74 metabolomics of TB vs healthy (Part 2: Serum)
STUDY_TYPE
Metabolomic analysis of TB vs healthy including time to TB.
STUDY_SUMMARY
Within the GC6-74 cohorts, 4,462 HIV-negative healthy household contacts of 1,098 index TB cases were recruited from 2006 to 2012 at four African sites included in this study i.e. SUN (Stellenbosch University, South Africa), MRC (Medical Research Council Unit, The Gambia), AHRI (Armauer Hansen Research Institute, Ethiopia) and MAK (Makerere University, Uganda). The study had an exclusion period of 3 months, such that participants, who were diagnosed with active TB within 3 months of enrolment, were excluded from analysis to prevent inclusion of participants who had incipient or asymptomatic clinical TB disease at enrolment. Additional exclusion criteria were positive HIV rapid test, current or previous anti-retroviral treatment, history of TB, pregnancy, participation in drug and/or vaccine clinical trials and chronic disease diagnosis or immunosuppressive therapy within the past 6 months, and living in the study area for less than 3 months. A total of 97 individuals who developed active TB within the two year follow-up period were included in this study and matched at a ratio of 1:4 with participants who remained healthy during the 2-year follow-up period (controls); matching, by site, age class, sex, and wherever possible year of recruitment. Initial samples collected upon enrolment were termed baseline (BL) samples. Further samples were taken 6 and 18 months post-exposure, provided that the participant had remained TB free at the time of sample collection. Metabolic profiling was carried out for each study site, using either serum or plasma samples. For a small number of samples, an insufficient amount of plasma was available, so the sample was diluted using RPMI buffer.
Metabolomic analysis of TB vs heathy including time to TB.
STUDY_SUMMARY
Within the GC6-74 cohorts, 4,462 HIV-negative healthy household contacts of 1,098 index TB cases were recruited from 2006 to 2012 at four African sites included in this study i.e. SUN (Stellenbosch University, South Africa), MRC (Medical Research Council Unit, The Gambia), AHRI (Armauer Hansen Research Institute, Ethiopia) and MAK (Makerere University, Uganda). The study had an exclusion period of 3 months, such that participants, who were diagnosed with active TB within 3 months of enrolment, were excluded from analysis to prevent inclusion of participants who had incipient or asymptomatic clinical TB disease at enrolment. Additional exclusion criteria were positive HIV rapid test, current or previous anti-retroviral treatment, history of TB, pregnancy, participation in drug and/or vaccine clinical trials and chronic disease diagnosis or immunosuppressive therapy within the past 6 months, and living in the study area for less than 3 months. A total of 97 individuals who developed active TB within the two year follow-up period were included in this study and matched at a ratio of 1:4 with participants who remained healthy during the 2-year follow-up period (controls); matching, by site, age class, sex, and wherever possible year of recruitment. Initial samples collected upon enrolment were termed baseline (BL) samples. Further samples were taken 6 and 18 months post-exposure, provided that the participant had remained TB free at the time of sample collection. Metabolic profiling was carried out for each study site, using either serum or plasma samples. For a small number of samples, an insufficient amount of plasma was available, so the sample was diluted using RPMI buffer.
Identification of unique metabolite networks between Latino and Caucasian patients with nonalcoholic fatty liver disease (NAFLD)
STUDY_TYPE
Populations comparison
STUDY_SUMMARY
Nonalcoholic fatty liver disease (NAFLD) is a spectrum of liver pathology ranging from simple steatosis to nonalcoholic steatohepatitis (NASH); the latter is characterized by inflammation and fibrosis. Risk factors for NALFD include obesity, diabetes, hyperlipidemia, and hypertension—all of which are features of metabolic syndrome. NAFLD is a very heterogeneous disease, as it presents in different patterns in males and females and in patients from different ethnicities, with unclear predictors for development and severity of disease. Previous studies have shown that NAFLD is 1.4 times more frequent in Hispanics than in Caucasians. One of the major challenges in NAFLD is the lack of accurate, noninvasive biomarkers for the detection of the most aggressive presentation, NASH. The gold standard for the diagnosis is liver biopsy, which is an invasive procedure associated with possible complications. Noninvasive diagnosis of NASH is a major unmet medical need and there are no ethnicity-specific biomarkers that can diagnose this condition and predict its progression. Therefore, the main gap in knowledge that this proposal and line of research will address is the characterizing the different plasma and liver metabolomics profile of patients with fatty liver from two ethnicities (Latinos vs. Caucasians) and of both sexes. The overall hypothesis of the present study is that the higher incidence of nonalcoholic fatty liver (NAFL) in Latino patients is reflected in a different plasma and liver metabolomics profile compared to Caucasian patients with further sex-related differences. Characterization of metabolite networks can aid in identifying the mechanistic underpinnings of sex and ethnic driven differences in NAFL which could help diagnose and establish a prognosis of this condition, especially in the critical transition from NAFL to the more aggressive nonalcoholic steatohepatitis (NASH).To address this hypothesis, plasma metabolomics profile of samples from male and female Latino and Caucasian bariatric surgery patients with NAFL and from healthy subjects will be compared. Metabolomics findings will be related with liver pathology and liver transcriptome profiles from intraoperatively obtained liver biopsies using correlation, network, and pathway analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomics biomarkers and the risk of overall mortality and ESRD in CKD: results from the Progredir Cohort.
STUDY_TYPE
ongoing cohort study
STUDY_SUMMARY
454 CKD participants were originally recruited from the outpatient services from Hospital das Clinicas, Sao Paulo. Extensive baseline data and biobank were collected between 2012-2013 in the Clinical Research Center, Universitary Hospital, Sao Paulo. Participants are being actively followed for events of mortality, renal replacement therapy and CVD. Death certificates are obtained from State and National Registries. For the this uploaded data, events were determined up to May 2017 (median follow-up time of 3 y). Censoring data was considered as the last day of contact.
INSTITUTE
Sao Paulo University
DEPARTMENT
Clinical Research Center, Universitary Hospital, Sao Paulo University
LABORATORY
Laboratory of Genetics and Molecular Cardiology, Heart Institute
LAST_NAME
Titan
FIRST_NAME
Silvia
ADDRESS
255 Av Dr Eneas Carvalho Aguiar, Cerqueira César, Sao Paulo, Sp, Brazil, 05403-000
EMAIL
smotitan@gmail.com
PHONE
+1-413-362-4377
TOTAL_SUBJECTS
451
STUDY_COMMENTS
Events are overall mortality, RRT, and a composite outcome of mortality and RRT. In addition, we also provided the variable for competitive data analysis (RRT considering the competing effect of death). Please see below for description of Study Design. Cox_mortality: death events (for Cox proportional hazard models) Cox_RRT: renal replacement therapy events (for Cox proportional hazard models) Cox_composite_deathRRT: death events AND renal replacement therapy events (for Cox proportional hazard models) Competitive_RRTvs death: death or renal replacement therapy events (for competitive risk analysis) Time_death: follow-up time for death events and censored-participants (for Cox models) Time_Cox_RRT: follow-up time for renal replacement therapy events and censored-participants (for Cox models) Time_composite_deathRRT: follow-up time for death AND renal replacement therapy and censored-participants (for Cox models) Time_competitive_TRSvsDeath: follow-up time for renal replacement therapy, death or censored-participants (for competitive analysis)
Metabolomic profiles in healthy research cats receiving clindamycin with a synbiotic or a placebo: a randomized, controlled trial
STUDY_TYPE
Double-blind randomized controlled trial
STUDY_SUMMARY
Antibiotic-associated gastrointestinal signs (AAGS) occur commonly in cats. Co-administration of synbiotics is associated with decreased AAGS in people, potentially due to stabilization of the fecal microbiome and metabolome. The purpose of this double-blinded randomized-controlled trial was to compare AAGS and the fecal microbiome and metabolome between healthy cats that received clindamycin with a placebo or synbiotic. Methods. 16 healthy domestic shorthair cats from a research colony were randomized to receive 150 mg clindamycin with either a placebo (8 cats) or commercially-available synbiotic (8 cats) once daily for 21 days with reevaluation 603 days thereafter. All cats ate the same diet. Food consumption, vomiting, and fecal score were recorded. Fecal samples were collected daily on the last 3 days of baseline (days 5-7), treatment (26-28), and recovery (631-633). Sequencing of 16S rRNA genes and gas chromatography time-of-flight mass spectrometry was performed. Clinical signs, alpha and beta diversity metrics, dysbiosis indices, proportions of bacteria groups, and metabolite profiles were compared between treatment groups using repeated measures ANOVAs. Fecal metabolite pathway analysis was performed. P<0.05 was considered significant. The Benjamini & Hochberg’s False Discovery Rate was used to adjust for multiple comparisons. Results. Median age was 6 and 5 years, respectively, for cats in the placebo and synbiotic groups. Hyporexia, vomiting, diarrhea, or some combination therein were induced in all cats. Though vomiting was less in cats receiving a synbiotic, the difference was not statistically significant. Bacterial diversity decreased significantly on days 26-28 in both treatment groups. Decreases in Actinobacteria (Bifidobacterium, Collinsella, Slackia), Bacteriodetes (Bacteroides), Lachnospiraceae (Blautia, Coprococcus, Roseburia), Ruminococcaceae (Faecilobacterium, Ruminococcus), and Erysipelotrichaceae (Bulleidia, [Eubacterium]) and increases in Clostridiaceae (Clostridium) and Proteobacteria (Aeromonadales, Enterobacteriaceae) occurred in both treatment groups, with incomplete normalization by days 631-633. Derangements in short-chain fatty acid, bile acid, indole, sphingolipid, benzoic acid, cinnaminic acid, and polyamine profiles also occurred, some of which persisted through the terminal sampling timepoint and differed between treatment groups. Discussion. Cats administered clindamycin commonly develop AAGS, as well as short- and long-term dysbiosis and alterations in fecal metabolites. Despite a lack of differences in clinical signs between treatment groups, significant differences in their fecal metabolomic profiles were identified. Further investigation is warranted to determine whether antibiotic-induced dysbiosis is associated with an increased risk of future AAGS or metabolic diseases in cats and whether synbiotic administration ameliorates this risk.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
16 subjects/3 timepoints/47 samples
STUDY_COMMENTS
Samples from 1 subject lacking for one timepoint, resulting in a total of 47 samples. Genomic DNA was extracted from 100 mg of feces from each pooled sample using a commercially available kit (PowerSoil®, Mo Bio, Carlsbad, CA USA) according to manufacturer’s protocol for a total of 11 pooled samples.
Metabolomic Analysis of plasma samples from Non-Allergic Subjects and Profilin-Allergic Patients overexposed to Grass Pollen
STUDY_TYPE
Allergy severity comparison
STUDY_SUMMARY
Prevalence and severity of allergic diseases have increased worldwide. To date, respiratory allergy phenotypes are not fully characterized and, along with inflammation progression, treatment is increasingly complex and expensive. Profilin sensitization constitutes a good model to study the progression of allergic inflammation. Our aim was to identify the underlying mechanisms and the associated biomarkers of this progression, focusing on severe phenotypes, using transcriptomics and metabolomics. Methods: 25 subjects were included in the study. Plasma samples were analyzed using Gas and Liquid Chromatography coupled to Mass Spectrometry (GC-MS and LC-MS, respectively). Individuals were classified in 4 groups – “non-allergic”, “mild”, “moderate” and “severe” – based on their clinical history, their response to an oral challenge test with profilin, and after a refinement using a mathematical metabolomic model. PBMCs were used for microarray analysis.
INSTITUTE
The Centre of Metabolomics and Bioanalysis
DEPARTMENT
Analytical chemistry
LAST_NAME
Obeso Montero
FIRST_NAME
David
ADDRESS
Avda. Monteprincipe s/n 28668 Boadilla del Monte, Madrid, España
Metabolomic profiles in healthy research cats receiving clindamycin with a synbiotic or a placebo: a randomized, controlled trial
STUDY_TYPE
Double-blind randomized controlled trial
STUDY_SUMMARY
Antibiotic-associated gastrointestinal signs (AAGS) occur commonly in cats. Co-administration of synbiotics is associated with decreased AAGS in people, potentially due to stabilization of the fecal microbiome and metabolome. The purpose of this double-blinded randomized-controlled trial was to compare AAGS and the fecal microbiome and metabolome between healthy cats that received clindamycin with a placebo or synbiotic. Methods. 16 healthy domestic shorthair cats from a research colony were randomized to receive 150 mg clindamycin with either a placebo (8 cats) or commercially-available synbiotic (8 cats) once daily for 21 days with reevaluation 603 days thereafter. All cats ate the same diet. Food consumption, vomiting, and fecal score were recorded. Fecal samples were collected daily on the last 3 days of baseline (days 5-7), treatment (26-28), and recovery (631-633). Sequencing of 16S rRNA genes and gas chromatography time-of-flight mass spectrometry was performed. Clinical signs, alpha and beta diversity metrics, dysbiosis indices, proportions of bacteria groups, and metabolite profiles were compared between treatment groups using repeated measures ANOVAs. Fecal metabolite pathway analysis was performed. P<0.05 was considered significant. The Benjamini & Hochberg’s False Discovery Rate was used to adjust for multiple comparisons. Results. Median age was 6 and 5 years, respectively, for cats in the placebo and synbiotic groups. Hyporexia, vomiting, diarrhea, or some combination therein were induced in all cats. Though vomiting was less in cats receiving a synbiotic, the difference was not statistically significant. Bacterial diversity decreased significantly on days 26-28 in both treatment groups. Decreases in Actinobacteria (Bifidobacterium, Collinsella, Slackia), Bacteriodetes (Bacteroides), Lachnospiraceae (Blautia, Coprococcus, Roseburia), Ruminococcaceae (Faecilobacterium, Ruminococcus), and Erysipelotrichaceae (Bulleidia, [Eubacterium]) and increases in Clostridiaceae (Clostridium) and Proteobacteria (Aeromonadales, Enterobacteriaceae) occurred in both treatment groups, with incomplete normalization by days 631-633. Derangements in short-chain fatty acid, bile acid, indole, sphingolipid, benzoic acid, cinnaminic acid, and polyamine profiles also occurred, some of which persisted through the terminal sampling timepoint and differed between treatment groups. Discussion. Cats administered clindamycin commonly develop AAGS, as well as short- and long-term dysbiosis and alterations in fecal metabolites. Despite a lack of differences in clinical signs between treatment groups, significant differences in their fecal metabolomic profiles were identified. Further investigation is warranted to determine whether antibiotic-induced dysbiosis is associated with an increased risk of future AAGS or metabolic diseases in cats and whether synbiotic administration ameliorates this risk.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
16 subjects/3 timepoints/43 samples
STUDY_COMMENTS
Samples from 5 cats (4 placebo, 1 synbiotic) were not available at the second timepoint due to withdrawal from treatment due to severity of gastrointestinal signs. Genomic DNA was extracted from 100 mg of feces from each pooled sample using a commercially available kit (PowerSoil®, Mo Bio, Carlsbad, CA USA) according to manufacturer’s protocol for a total of 11 pooled samples.
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (Part I)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part II)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part III)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part IV)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part V)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part VI)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part VII)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part VIII)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography−High-Resolution Mass Spectrometry Platforms (part IX)
STUDY_SUMMARY
Liquid chromatography−mass spectrometry (LC−MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC−MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolomic Markers of Dietary Patterns in the Costa Rica Study
STUDY_TYPE
MS analysis
STUDY_SUMMARY
The study will examine associations between dietary patterns and the metabolome on a random subset (n=80) of control subjects in a population-based case-control study of myocardial infarction in Costa Rican adults. Each sample will undergo complementary LC-MS-based approaches, specifically untargeted metabolite profiling and targeted lipidomic profiling. Subsequently we will test for associations between 1) previously derived dietary patterns and plasma molecular features and 2) the top plasma correlates of dietary patterns and metabolic syndrome.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Amino Acid Concentrations of Primary Sclerosing Cholangitis (part I)
STUDY_SUMMARY
To qualitatively and quantitatively analyze enterohepatically-circulated molecules using targeted amino acid concentrations of peripheral blood collected from primary sclerosing cholangitis (PSC) patients compared to normal and diseased controls. There are three groups of patients. (1) Normal donor controls (ND), (2) Patients with Primary Sclerosing Cholangitis (PSC), and (3) Disease Controls (DC) which are patients with liver disease other than PSC.
INSTITUTE
Mayo Clinic
LAST_NAME
O'Hara
FIRST_NAME
Steven
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Non-Esterified Fatty Acids of Primary Sclerosing Cholangitis (part II)
STUDY_SUMMARY
To qualitatively and quantitatively analyze enterohepatically-circulated molecules using targeted free fatty acid concentrations of peripheral blood collected from primary sclerosing cholangitis (PSC) patients compared to normal and diseased controls. There are three groups of patients. (1) Normal donor controls (ND), (2) Patients with Primary Sclerosing Cholangitis (PSC), and (3) Disease Controls (DC) which are patients with liver disease other than PSC.
INSTITUTE
Mayo Clinic
LAST_NAME
O'Hara
FIRST_NAME
Steven
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Acyl Carnitines Concentrations of Primary Sclerosing Cholangitis (part III)
STUDY_SUMMARY
To qualitatively and quantitatively analyze enterohepatically-circulated molecules using targeted acyl carnitines concentrations of peripheral blood collected from primary sclerosing cholangitis (PSC) patients compared to normal and diseased controls. There are three groups of patients. (1) Normal donor controls (ND), (2) Patients with Primary Sclerosing Cholangitis (PSC), and (3) Disease Controls (DC) which are patients with liver disease other than PSC.
INSTITUTE
Mayo Clinic
LAST_NAME
O'Hara
FIRST_NAME
Steven
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Bile Acid of Primary Sclerosing Cholangitis (part IV)
STUDY_SUMMARY
To qualitatively and quantitatively analyze enterohepatically-circulated molecules using targeted bile acid concentrations of peripheral blood collected from primary sclerosing cholangitis (PSC) patients compared to normal and diseased controls. There are three groups of patients. (1) Normal donor controls (ND), (2) Patients with Primary Sclerosing Cholangitis (PSC), and (3) Disease Controls (DC) which are patients with liver disease other than PSC.
INSTITUTE
Mayo Clinic
LAST_NAME
O'Hara
FIRST_NAME
Steven
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels
STUDY_TYPE
Metabolomics in C. elegans
STUDY_SUMMARY
Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode Caenorhabditis elegans. We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA and AA levels with a heritability ranging from 32-82%. We detected strongly co-correlated metabolite clusters and 36 significant metabolite QTL (mQTL). We focused on mQTL displaying highly significant linkage and heritability, including an mQTL for the FA C14:1 on Chromosome I, and another mQTL for the FA C18:2 on Chromosome IV. Using introgression lines (ILs) we were able to narrow down both mQTL to a 1.4 Mbp and a 3.6 Mbp region, respectively. RNAi-based screening focusing on the Chromosome I mQTL identified several candidate genes for the C14:1 mQTL, including lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81. Overall, this systems approach provides us with a powerful platform to study the genetic basis of C. elegans metabolism. Furthermore, it allows us to investigate interventions, such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis, and identify gene-by-environment interactions.
INSTITUTE
Academic Medical Center of Amsterdam
LAST_NAME
Gao
FIRST_NAME
Arwen
ADDRESS
Meibergdreef 9, Amsterdam, North-Holland, 1105 AZ, Netherlands
Gut microbiome structure and metabolic activity in inflammatory bowel disease
STUDY_SUMMARY
The inflammatory bowel diseases (IBD), which include Crohn’s disease (CD) and ulcerative colitis (UC), are multifactorial, chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome -- the molecular interface between host and microbiota -- are less-well understood. To address this gap, we performed untargeted LC-MS metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n=155) and validation (n=65) cohorts of CD, UC, and non-IBD control subjects. Metabolomic and metagenomic profiles were broadly correlated with fecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant (DA) in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While >50% of DA metabolite features were uncharacterized, many could be assigned putative roles through metabolomic “guilt-by-association” (covariation with known metabolites). DA species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between DA species and well-characterized DA metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.
Untargeted high-resolution mass spectrometry profiling
STUDY_SUMMARY
Urban environments remain a poorly understood toxic environment for children with asthma, where improved exposure characterization and estimation of exposurehealth outcome relationships are clearly needed. The goal of this project is to investigate the interactions between relevant environmental exposures and asthma severity in a year-long longitudinal study of urban children with asthma. Environmental and clinical samples are being collected at 3 seasonal visits. Using these samples, we will measure the effects of multiple relevant exposures (environmental tobacco smoke (ETS), polycyclic aromatic hydrocarbons (PAHs), phthalates, and volatile organic compounds (VOCs)) on biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids) and asthma outcomes. Our overall hypothesis is that relevant environmental exposures and their interactions drive disease severity in urban children with asthma. We will test this hypothesis by investigating the following aims: Aim 1: To investigate how environmental exposures (ETS, PAHs, phthalates, and VOCs) and their interactions contribute to asthma severity in urban children. Aim 2: To determine if environmental exposures in children with asthma are associated with changes in in biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids). Aim 3: To determine which biological responses mediate the relationships between environmental exposures and asthma severity. Aim 4: To compare environmental exposures and biological responses in asthmatic and non-asthmatic children
INSTITUTE
Emory University
DEPARTMENT
School of Medicine
LABORATORY
Clincal Biomarkers Laboratory
LAST_NAME
Uppal
FIRST_NAME
Karan
ADDRESS
615 Michael St. Ste 225, Atlanta, GA, 30322, USA
EMAIL
kuppal2@emory.edu
PHONE
(404) 727 5027
TOTAL_SUBJECTS
66
STUDY_COMMENTS
Both CHEAR and Clinical Biomarker Laboratory pooled plasma samples were used for quality control. Study specific sample pools were not created
Amino Acid Concentrations in Muscle Tissue of Muscle Wasting in Cancer Cachexia (part I)
STUDY_SUMMARY
Amino Acid Concentrations of Muscle Wasting in Cancer Cachexia. Muscle samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
TCA Concentrations in Muscle Tissue of Muscle Wasting in Cancer Cachexia (part II)
STUDY_SUMMARY
TCA Concentrations of Muscle Wasting in Cancer Cachexia. Muscle samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Multi-Platform Physiologic and Metabolic Phenotyping Reveals Microbial Toxicity (part II)
STUDY_SUMMARY
The gut microbiota are susceptible to modulation by environmental stimuli and therefore can serve as biological sensors. Recent evidence suggests that xenobiotics can disrupt the interaction between the microbiota and host. Here, we describe an approach that combines in vitro microbial incubation (isolated cecal contents from mice), flow cytometry, and mass spectrometry- and 1H NMR-based metabolomics to evaluate xenobiotic-induced microbial toxicity. Tempol, a stabilized free radical scavenger known to remodel the microbial community structure and function in vivo, was studied to assess its direct effects on the gut microbiota. Microbiota were isolated from mouse cecum and were exposed to tempol for 4 h under strict anaerobic condition. The flow cytometry data suggested short term exposure of the microbiota to tempol is associated with disrupted membrane physiology as well as compromised metabolic activity. Mass spectrometry and NMR metabolomics revealed that tempol exposure significantly disrupted microbial metabolic activity, specifically indicated by changes in short chain fatty acids, branched chain amino acids, amino acids, nucleotides, glucose, and oligosaccharides. In addition, a mouse study with tempol (5 days gavage) showed similar microbial physiologic and metabolic changes, indicating the in vitro approach reflected in vivo conditions. Our results, through evaluation of microbial viability, physiology and metabolism, and comparison of in vitro and in vivo exposures with tempol, suggests that physiologic and metabolic phenotyping provides unique insight into gut microbiota toxicity.
INSTITUTE
The Pennsylvania State University (Penn State)
LAST_NAME
Nichols
FIRST_NAME
Robert
ADDRESS
650 toftrees ave Apt #108, State College, Pa 16802
Acyl Carnitines Concentrations in Muscle Tissue of Muscle Wasting in Cancer Cachexia (part-IV)
STUDY_SUMMARY
Acyl Carnitines Concentrations of Muscle Wasting in Cancer Cachexia. Muscle samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
NEFA Panel in Muscle Tissue of Muscle Wasting in Cancer Cachexia (part-V)
STUDY_SUMMARY
NEFA Panel of Muscle Wasting in Cancer Cachexia. Muscle samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
NEFA Panel in Serum for Muscle Wasting in Cancer Cachexia (part-VI)
STUDY_SUMMARY
NEFA Panel of Muscle Wasting in Cancer Cachexia. Serum samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Amino Acid Concentrations in Serum for Muscle Wasting in Cancer Cachexia (part-VII)
STUDY_SUMMARY
Amino Acid Concentrations of Muscle Wasting in Cancer Cachexia. Serum samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
TCA Concentrations in Serum for Muscle Wasting in Cancer Cachexia (part-VIII)
STUDY_SUMMARY
TCA Concentrations of Muscle Wasting in Cancer Cachexia. Serum samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Sphingolipid Concentrations in Serum for Muscle Wasting in Cancer Cachexia (part-IX)
STUDY_SUMMARY
Sphingolipid Concentrations of Muscle Wasting in Cancer Cachexia. Serum samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Acyl Carnitines Concentration in Serum for Muscle Wasting in Cancer Cachexia (part-X)
STUDY_SUMMARY
Acyl Carnitines Concentrations of Muscle Wasting in Cancer Cachexia. Serum samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Sphingolipid Concentrations in Muscle Tissue of Muscle Wasting in Cancer Cachexia (part-III)
STUDY_SUMMARY
Sphingolipid Concentrations of Muscle Wasting in Cancer Cachexia. Muscle samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Large Scale Profling in Muscle Tissue for Muscle Wasting in Cancer Cachexia (part-XI)
STUDY_SUMMARY
Large Scale Profiling of muscle wasting in Cancer Cachexia. Muscle samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Large Scale Profiling in Serum for Muscle Wasting in Cancer Cachexia (part-XII)
STUDY_SUMMARY
Large Scale Profiling of muscle wasting in Cancer Cachexia. Serum samples from 10 control patients, 10 weight stable pancreatic cancer patients, and 10 pancreatic cancer patients with significant weight loss. Samples are divided evenly between males and females.
INSTITUTE
Mayo Clinic
LAST_NAME
Guttridge
FIRST_NAME
Denis
ADDRESS
520 Biomedical Research Tower 460 W. 12th Avenue Columbus, OH 43210
Lipidomic profiling of heart and plasma of mice following swim training versus pressure overload
STUDY_SUMMARY
Lipid profiling was performed on hearts and plasma from mice subjected to a physiological stimulus (4 weeks of swim exercise training) or pathological stimulus (4 weeks of pressure overload – transverse aortic constriction; TAC)
Characterization of metabolomics profile changes during development of post-traumatic epilepsy in Rat Plasma (part-I)
STUDY_SUMMARY
Characterize the metabolomics profile changes during progression of the transition from traumatic brain injury (TBI) to post-traumatic epilepsy (PTE). To do so, three experiments will be performed. PTE animal model will be developed using ferrous chloride injections. Metabolomics profile changes will be obtained before TBI, after TBI, and after PTE development These temporal changes in metabolomics profile during the course of PTE development will be collected. We will also collect cerebrospinal fluid (CSF) at each time point. In addition, we will collect the brain tissue from the center of injury, around the injury, and from the non-injured area for mass spectrometry. In this study, the rat plasma at each time point is analyzed.
Characterization of metabolomics profile changes during development of post-traumatic epilepsy in Rat Cerebrospinal Fluid (part-II)
STUDY_SUMMARY
Characterize the metabolomics profile changes during progression of the transition from traumatic brain injury (TBI) to post-traumatic epilepsy (PTE). To do so, three experiments will be performed. PTE animal model will be developed using ferrous chloride injections. Metabolomics profile changes will be obtained before TBI, after TBI, and after PTE development These temporal changes in metabolomics profile during the course of PTE development will be collected. We will also collect cerebrospinal fluid (CSF) at each time point. In addition, we will collect the brain tissue from the center of injury, around the injury, and from the non-injured area for mass spectrometry. In this study, Rat CSF is analyzed at end of study.
Characterization of metabolomics profile changes during development of post-traumatic epilepsy in Rat Brain Tissue (part-III)
STUDY_SUMMARY
Characterize the metabolomics profile changes during progression of the transition from traumatic brain injury (TBI) to post-traumatic epilepsy (PTE). To do so, three experiments will be performed. PTE animal model will be developed using ferrous chloride injections. Metabolomics profile changes will be obtained before TBI, after TBI, and after PTE development These temporal changes in metabolomics profile during the course of PTE development will be collected. We will also collect cerebrospinal fluid (CSF) at each time point. In addition, we will collect the brain tissue from the center of injury, around the injury, and from the non-injured area for mass spectrometry. In this study, the rat brain tissue at end of study is analyzed.
H3K27M cells and glutamine metabolomics 1 million cell test (part-I)
STUDY_SUMMARY
Testing TCA concentrations of Diffuse Intrinsic Pontine Gliomas (DIPG) cellines with H3K27M mutations. One million cells are tested with a TCA concentrations panel. We are a high volume center for treating malignant gliomas, which gives us an advantage in obtaining tissue for these relatively rare tumors. We have developed several DIPG patient derived cell lines and xenografts that bear all the key molecular features of this disease including the H3K27M mutation and global H3K27 hypomethylation. These cells are low in passage and we think these lines more closely resemble the patients tumor pathology then established cell lines that have been in culture/mice for numerous years.
TCA cycle metabolomics of H3K27M cells grown in regular glutamine media, glutamine free media, and glutamine free media with alpha-ketoglutarate (Part-II)
STUDY_SUMMARY
Testing TCA concentrations of Diffuse Intrinsic Pontine Gliomas (DIPG) cellines with H3K27M mutations. Preliminary studies show H3K27M tumor cells are addicted to Gln for survival. Removal of Gln from media resulted in tumor cell death which was rescued by the addition of α-KG. These data show that Gln is taken up and metabolized by H3K27M tumor cells and that Gln derived α-KG is critical for the survival of these tumors. Interestingly, tumor cell death with Gln deprivation was similar to the effect of the JMJD3 inhibitor GSKJ4. Therefore, Gln derived α-KG may be required for both anaplerosis and to drive JMJD3 demethylation. We hypothesize that H3K27M tumors are reliant on α-KG that is derived from Gln to drive the TCA cycle and further decrease H3K27 methylation levels. Furthermore, inhibition of Gln metabolism may represent a novel therapeutic approach for tumors with this mutation. In this study, TCA cycle metabolomics are analyzed of H3K27M cells grown in regular glutamine media, glutamine free media, and glutamine free media with alpha-ketoglutarate.
TCA Isotopmer metabolomics of H3K27M Cells grown in regular media, glutamine enriched regular media, and glucose encriched regular media (Part-III)
STUDY_SUMMARY
TCA Isotopmer metabolomics of H3K27M Cells grown in regular media, glutamine enriched regular media, and glucose encriched regular media. TCA isotopomers traced for 0, 12, or 24 hours were measured.
TCA cycle metabolomics of H3K27M Cell Nucleus Fraction and Cell Mitonchonrdial Fraction (Part-IV)
STUDY_SUMMARY
Testing TCA concentrations of Diffuse Intrinsic Pontine Gliomas (DIPG) cellines with H3K27M mutations. Preliminary studies show H3K27M tumor cells are addicted to Gln for survival. Removal of Gln from media resulted in tumor cell death which was rescued by the addition of α-KG. These data show that Gln is taken up and metabolized by H3K27M tumor cells and that Gln derived α-KG is critical for the survival of these tumors. Interestingly, tumor cell death with Gln deprivation was similar to the effect of the JMJD3 inhibitor GSKJ4. Therefore, Gln derived α-KG may be required for both anaplerosis and to drive JMJD3 demethylation. We hypothesize that H3K27M tumors are reliant on α-KG that is derived from Gln to drive the TCA cycle and further decrease H3K27 methylation levels. Furthermore, inhibition of Gln metabolism may represent a novel therapeutic approach for tumors with this mutation. In this study, TCA cycle metabolomics are analyzed of H3K27M cells grown in regular glutamine media, glutamine free media, and glutamine free media with alpha-ketoglutarate. Additionally, cell nucleus and cell mitochrondial fractions are run separately.
Influence of Data-Processing Strategies on Normalized Lipid Levels using an Open-Source LC-HRMS/MS Lipidomics Workflow
STUDY_SUMMARY
Lipidomics is an emerging field with significant potential for improving clinical diagnosis and our understanding of health and disease. While the diverse biological roles of lipids contribute to their clinical utility, the unavailability of lipid internal standards representing each species, make lipid quantitation analytically challenging. The common approach is to employ one or more internal standards for each lipid class examined and use a single point calibration for normalization (relative quantitation). To aid in standardizing and automating this relative quantitation process, we developed LipidMatch Normalizer (LMN) http://secim.ufl.edu/secim-tools/ which can be used in most open source lipidomics workflows. While the effect of lipid structure on relative quantitation has been investigated, applying LMN we show that data-processing can significantly affect lipid semi-quantitative amounts. Polarity and adduct choice had the greatest effect on normalized levels; when calculated using positive versus negative ion mode data, one fourth of lipids had greater than 50 % difference in normalized levels. Based on our study, sodium adducts should not be used for statistics when sodium is not added intentionally to the system, as lipid levels calculated using sodium adducts did not correlate with lipid levels calculated using any other adduct. Relative quantification using smoothing versus not smoothing, and peak area versus peak height, showed minimal differences, except when using peak area for overlapping isomers which were difficult to deconvolute. By characterizing sources or variation introduced during data-processing and introducing automated tools, this work helps increase through-put and improve data-quality for determining relative changes across groups.
INSTITUTE
University of Florida
DEPARTMENT
Chemistry
LABORATORY
Richard Yost Laboratory
LAST_NAME
Levy
FIRST_NAME
Allison
ADDRESS
214 Leigh Hall, PO Box 117200, Gainesville, Florida, 32611, USA
Metabolic profiling of identified single cells in Xenopus laevis embryos
STUDY_TYPE
Metabolic profiling of single cells
STUDY_SUMMARY
Single D11 cells were identified in 16-cell embryos of Xenopus laevis. Metabolites were extracted, and the extracts were analyzed using a custom-built capillary electrophoresis electrospray ionization platform coupled to a quadrupole time-of-flight mass spectrometer. The resulting metadata was analyzed by Trace, a custom-design software, designed to extract molecular feautres from trace-sensitive metabolomics experiments. The results were validated against molecular features that were extracted by manual curation of the same raw mass spectrometer files.
INSTITUTE
University of Maryland
DEPARTMENT
Department of Chemistry & Biochemistry
LABORATORY
Nemes Laboratory
LAST_NAME
Nemes
FIRST_NAME
Peter
ADDRESS
0107 Chemistry Building, 8051 Regents Dr, College Park, MD 20742
EMAIL
nemes@umd.edu
PHONE
3014050373
NUM_GROUPS
5 biological replicates (different cells from different embryos) + 1-to-3 technical replicates (same extract analyzed multiple times)
TOTAL_SUBJECTS
5 different D11 cells were analyzed, each from a different embryo
PUBLICATIONS
Trace: Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry – A Case Study from Single-Cell Metabolomics
An integrated, high-throughput strategy for multi-omic systems level analysis
STUDY_SUMMARY
This report details the automation, benchmarking, and application of a strategy for transcriptomic, proteomic, and metabolomic analyses from a common sample. The approach, Sample Preparation for multi-Omics Technologies (SPOT), provides equivalent performance to typical individual omic preparation methods, but it greatly enhances throughput and minimizes the resources required for multi-omic experiments. SPOT was applied to a multi-omics time course experiment for zinc-treated HL60 cells.
Untargeted Discovery in Primary Metabolism: Collision Cross Section as a Molecular Descriptor in Ion Mobility Spectrometry
STUDY_TYPE
Database Library
STUDY_SUMMARY
In this work we have established a collision cross section (CCS) library of primary metabolites based on analytical standards in the Mass Spectrometry Metabolite Library of Standards (MSMLS). Using a commercially available ion mobility-mass spectrometer (IM-MS, Agilent 6560), from the 554 unique compounds in the MSMLS plate library we obtained a total of 1246 CCS measurements over a wide range of biochemical classes and adduct types. Resulting data analysis showed that the curated CCS library provides broad molecular coverage of metabolic pathways and highlights intrinsic mass/mobility relationships for specific metabolite superclasses. The separation and characterization of isomeric metabolites were assessed as well as an investigation to determine the analytical separation efficiency in both the mass (m/z) and mobility (CCS/ΔCCS) dimension required for untargeted metabolomic analyses. To further demonstrate the analytical utility of CCS as an additional molecular descriptor, a well characterized biological sample of human plasma serum (NIST 1950) was examined by LC-IM-MS and a detailed analysis of carbohydrate isomers by ion mobility is presented.
INSTITUTE
Vanderbilt University
DEPARTMENT
Chemistry
LABORATORY
McLean Laboratory
LAST_NAME
Dodds
FIRST_NAME
James
ADDRESS
7330 Stevenson Ct., Nashville, Tennessee, 37235, USA
Metabolome analysis on multi-connected biparental chromosome segment substitution line populations in rice
STUDY_SUMMARY
rice flag leaves at heading stage from three chromosome substitution line populations, which were respectively constructed by introducing genomic segments from japonica cultivar Niponbare, indica cultivar Minghui 63 and wild accession ACC10, to an indica cultivar Zhenshan 97, were collected. Metabolomics profile was conducted to generate quantitative trait loci that may affect contents of metabolites, and candidate genes were assigned.
Single-cell Profiling of Cationic and Anionic Metabolites in Live Frog (Xenopus) Embryos using Microprobe Capillary Electrophoresis Mass Spectrometry
STUDY_TYPE
Metabolic profiling of single cells
STUDY_SUMMARY
The goal of this study was to enable the analysis of anionic and cationic metabolites from the same identified single cell in Xenopus laevis embryos. A 10 nL portion of identified animal-ventral (V1) cells was aspirated from 8-cell embryos, and metabolites were extracted from the aspirate, before characterization of cationic and anionic compounds using a custom-built capillary electrophoresis (CE) electrospray ionization (ESI) mass spectrometry platform. A total of ~250 cationic molecular features and ~150 anionic molecular features were detected, including 76 metabolites that were identified in this study. Pathway analysis of the identified metabolites highlighted arginine-proline metabolism of significance.
INSTITUTE
University of Maryland, College Park
DEPARTMENT
Department of Chemistry & Biochemistry
LABORATORY
Nemes Laboratory
LAST_NAME
Nemes
FIRST_NAME
Peter
ADDRESS
0107 Chemistry Building 8051 Regents Drive
EMAIL
nemes@umd.edu
PHONE
3014050373
NUM_GROUPS
4 biological replicates (each different cell from a different embryo) + 1-to-2 technical replicates (same extract analyzed multiple times)
TOTAL_SUBJECTS
4 different V1 cells were analyzed, each from a different embryo
Determination of mode of action of anti-malalrial drugs using untargeted metabolomics
STUDY_SUMMARY
The mode of action of a representative active compound was investigated using an unbiased metabolomics approach, which has previously been shown to reveal both novel and established modes of action of antimalarials (Creek et al 2016, DOI: 10.1128/AAC.01226-16). The active antimalarial OSM-S-313, and the inactive analogue OSM-S-291, were incubated with trophozoite stage P. falciparum parasites for five hours alongside reference compounds including atovaquone (ATV), chloroquine (CQ), dihydroartemisisin (DHA) and three PfATP4 inhibitors, MMV00073, MMV397264 and MMV390482. Metabolomics analysis of cell pellets and spent media allowed reproducible detection of diverse metabolites from a range of metabolic pathways, with the most significant OSM-S-313-induced perturbations observed within peptide, lipid and energy metabolism, suggesting a specific impact on parasite metabolism.
INSTITUTE
Monash University
LAST_NAME
Creek
FIRST_NAME
Darren
ADDRESS
Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
PAMP-triggered changes in the exometabolome of Arabidopsis suspension cells
STUDY_SUMMARY
The goal of this study was to determine how the exometabolome of defense-elicited Arabidopsis suspension cells inhibits virulence gene expression and growth of a plant pathogenic bacterium Pseudomonas syringae. Arabidopsis T87 suspension cells were treated with the pathogen-associated molecular pattern elf26 or a DMSO-control treatment for six hours, then incubated in fresh media for one hour. The conditioned medium (exudate) was collected from each culture by centrifugation and 0.22 um filter to remove plant cells. These samples are designated T=6 mock and T=6 elf26 in our experimental design. We also prepared samples in the same manner from control-treated cells except without any pre-treatment time prior to one hour exudate production. These samples are labeled T=0 mock. A total of seven biological replicates of each treatment condition were analyzed, with each replicate prepared from cells grown in separate flasks. The exudates were prepared in four independent experiments performed on separate days (1 biological replicate from first experiment, 2 biological replicates from each of the 3 remaining experiments). Four samples of the culture medium, one from each of the four independent experiments, are included.
TCA Isotopomers in Neuromyelitis Optica Patients (part - I)
STUDY_SUMMARY
Patients with an inflammatory disease of the central nervous system known as neuromyelitis optica (NMO) experience increased levels of depression. These patients have an antibody that recognizes a type of cell in the brain called astrocytes – binding of this antibody to astrocytes triggers a stress response in the cell that results in the development of brain lesions that cause disability and cognitive disturbances. We recently observed a change in the level of glutamate in a part of the brain involved in depression in patients with NMO. Glutamate is a chemical that is used in the brain for communication between neurons – reduced levels of glutamate are thought to trigger depression by reducing neuronal activity in specific circuits. Based on this observation and the known role of astrocytes in maintaining glutamate levels in the brain, we hypothesize that the NMO antibody disturbs metabolic activity in astrocytes and thereby reduces glutamate and triggers depression. We intend to trace the metabolic response induced in astrocytes by the NMO antibody using TCA isotopomers. It is our hope that we will not only learn something about the mechanisms of astrocyte dysregulation in neuromyelitis optica, but that we will learn something about the mechanisms of depression in general that may lead to new therapies for this disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Howe
FIRST_NAME
Charles
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
TCA Concentrations in Neuromyelitis Optica Patients (part - II)
STUDY_SUMMARY
Patients with an inflammatory disease of the central nervous system known as neuromyelitis optica (NMO) experience increased levels of depression. These patients have an antibody that recognizes a type of cell in the brain called astrocytes – binding of this antibody to astrocytes triggers a stress response in the cell that results in the development of brain lesions that cause disability and cognitive disturbances. We recently observed a change in the level of glutamate in a part of the brain involved in depression in patients with NMO. Glutamate is a chemical that is used in the brain for communication between neurons – reduced levels of glutamate are thought to trigger depression by reducing neuronal activity in specific circuits. Based on this observation and the known role of astrocytes in maintaining glutamate levels in the brain, we hypothesize that the NMO antibody disturbs metabolic activity in astrocytes and thereby reduces glutamate and triggers depression. We intend to measure TCA concentration in NMO astrocytes. It is our hope that we will not only learn something about the mechanisms of astrocyte dysregulation in neuromyelitis optica, but that we will learn something about the mechanisms of depression in general that may lead to new therapies for this disease.
INSTITUTE
Mayo Clinic
LAST_NAME
Howe
FIRST_NAME
Charles
ADDRESS
200 First St. SW, Rochester, Minnesota, 55905, USA
Denver Asthma Panel Study-CHEAR Ancillary Study (part II)
STUDY_SUMMARY
Urban environments remain a poorly understood toxic environment for children with asthma, where improved exposure characterization and estimation of exposurehealth outcome relationships are clearly needed. The goal of this project is to investigate the interactions between relevant environmental exposures and asthma severity in a year-long longitudinal study of urban children with asthma. Environmental and clinical samples are being collected at 3 seasonal visits. Using these samples, we will measure the effects of multiple relevant exposures (environmental tobacco smoke (ETS), polycyclic aromatic hydrocarbons (PAHs), phthalates, and volatile organic compounds (VOCs)) on biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids) and asthma outcomes. Our overall hypothesis is that relevant environmental exposures and their interactions drive disease severity in urban children with asthma. We will test this hypothesis by investigating the following aims: Aim 1: To investigate how environmental exposures (ETS, PAHs, phthalates, and VOCs) and their interactions contribute to asthma severity in urban children. Aim 2: To determine if environmental exposures in children with asthma are associated with changes in in biological responses (metabolomics, oxidative stress, inflammatory markers, and endocannabinoids). Aim 3: To determine which biological responses mediate the relationships between environmental exposures and asthma severity. Aim 4: To compare environmental exposures and biological responses in asthmatic and non-asthmatic children
INSTITUTE
Emory University
DEPARTMENT
School of Medicine
LABORATORY
Clincal Biomarkers Laboratory
LAST_NAME
Uppal
FIRST_NAME
Karan
ADDRESS
615 Michael St. Ste 225, Atlanta, GA, 30322, USA
EMAIL
kuppal2@emory.edu
PHONE
(404) 727 5027
TOTAL_SUBJECTS
169
STUDY_COMMENTS
Both CHEAR pooled urine samples and Clinical Biomarker Laboratory pooled plasma samples were used
Development of a weaned pig model of enterotoxigenic E.coli-induced environmental enteropathy
STUDY_TYPE
Animal Model
STUDY_SUMMARY
Environmental Enteropathy (EE) is a subclinical condition primarily effecting developing countries believed to be caused by chronic fecal-oral contamination. The condition is characterized by chronic gut inflammation, malabsorption, stunting of growth, stunted villi, and reduced efficacy of oral vaccines. Due to the similarity of the gastrointestinal tract and immune response of swine and humans, the piglet is an attractive model for studying this condition. In this present study, piglets were challenged with either a chronic or acute dose of pathogenic E.coli in an attempt to mimic the symptoms of EE over a 7 day trial period. Throughout the study a number of biological samples were collected for analysis and are presented here, including feces for untargeted metabolomics analysis.
Pediatric Inner-City Environmental Exposures at School and Home and Asthma Study
STUDY_TYPE
CHEAR Study
STUDY_SUMMARY
SICAS 1 and SICAS 2 have extraordinary opportunity to evaluate the role of diet, environmental exposures and asthma in the context of school and home specific exposures and capitalize on all the data we are already collecting. Asthma affects 25 million Americans, particularly urban minority children. Children spend nearly all day in school, yet little is known about the role of a child’s exposure to widely disseminated industrial chemicals on asthma morbidity. Early animal models and population studies have begun to identify an association between phenolic chemical exposure and asthma development through proposed increased regulation of an individual’s allergic immune response. This study, nested within a school-based environmental intervention trial, (School Inner-City Asthma Intervention Study, SICAS2) , will enable urinary biomarker analyses during a school-based academic year-long environmental intervention trial to analyze the source and impact of exposures on urinary environmental exposure biomarker levels as well as the relationship between these biomarkers levels and asthma morbidity. We are poised to leverage the clinical and exposure data being collected in the clinical trial and generate cross-sectional urinary phenol biomarker data (at baseline) within the resources of CHEAR. If successful, our study will assess the impact of exposures on these biomarker levels and the impact that these exposures have on asthma morbidity, controlling comprehensively for other personal, home, and school environmental factors associated with asthma outcomes. We hypothesize that exposure to environmental exposures (e.g. phenols, phthalates, environmental tobacco smoke) in urban school children and higher urinary biomarkers will preliminarily be associated with higher asthma morbidity. Specific aims are: Aim 1. To determine the source of exposure to environmental exposures (e.g. phenols, phthalates, environmental tobacco smoke) in inner-city school children as assessed by questionnaire, product use assessment and comprehensive school and home environmental assessment of children with physician-diagnosed asthma. Aim 2. To determine whether urinary phenol/phathalate/cotinine biomarkers are associated with asthma control (e.g. asthma symptoms, such as asthma-related symptom days (primary outcome), and other phenotypes of asthma/allergic symptoms and inflammation such as allergic sensitization, health care utilization and pulmonary lung function
INSTITUTE
Icahn School of Medicine at Mount Sinai
DEPARTMENT
Department of Environmental Medicine and Public Health
Two groups of rats were fed either a high salt diet or a low salt diet. This study aims to look at salt intake in correlation to altering other metabolites and the onset of hypertension
Lipidomics for wildlife disease etiology and biomarker discovery: a case study of pansteatitis outbreak in South Africa (part-I)
STUDY_TYPE
lipidomics
STUDY_SUMMARY
Lipidomics is a promising tool to determine biomarkers and elucidate mechanisms associated with anthropogenic-induced stress in wildlife. Therefore, we examine the application of lipidomics for in situ studies on Mozambique tilapia (Oreochromis mossambicus) in Loskop Dam, South Africa. Mortality events of aquatic life associated with an environmentally-derived inflammatory disease, pansteatitis, have occurred in this area. The lipidome of adipose tissue (n = 31) and plasma (n = 51) from tilapia collected from at Loskop Dam were characterized using state of the art liquid chromatography coupled to high-resolution tandem mass spectrometry. Lipid profiles reflected pansteatitis severity and were significantly different between diseased and healthy individuals. Over 13 classes of lipids associated with inflammation, cell death, and/or oxidative damage were upregulated in pansteatitis-affected adipose tissue, including ether-lipids, short-chained triglyceride oxidation products, sphingolipids, and acylcarnitines. Ceramides showed a 1000-fold increase in the most affected adipose tissues, illustrating its potential as sensitive and novel indicators of disease severity. In plasma, triglycerides were found to be downregulated in pansteatitis-affected tilapia. As comprehensive coverage of the lipidome aids in the elucidation of possible disease mechanisms, application of lipidomics could be applied to the understanding of other environmentally-derived inflammatory conditions, such as those caused by obesogens.
INSTITUTE
South East Center for Integrated Metabolomics
DEPARTMENT
Department of Pathology, Immunology and Laboratory Medicine
LABORATORY
SECIM
LAST_NAME
Koelmel
FIRST_NAME
Jeremy
ADDRESS
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, 1395 Center Dr, Room M641c
EMAIL
jeremykoelmel@gmail.com
PHONE
7187300454
NUM_GROUPS
8
TOTAL_SUBJECTS
51
NUM_MALES
28
NUM_FEMALES
23
STUDY_COMMENTS
Adipose and plasma do not overlap exactly in subjects ran
Evaluation of the short-term effects of the allelochemical umbelliferone on Triticum durum L. metabolism through GC-MS based untargeted metabolomics
STUDY_SUMMARY
Allelopathy is a plant defense mechanism by which they protect themselves from competitive species using specialized biochemicals in the form of secretion or volatiles released to the environment. Though, umbelliferone is a well-known allelochemical, its mechanism of action in a short-term treatment is far from established. We used ≈ 10–days old wheat seedlings treated with104 µM umbelliferone over a time course experiment covering 6 times points, i.e., 0h, 6h, 12h, 24h, 48h, and 96h and compared the metabolomic changes to control (mock-treated) plants. Using gas chromatography mass-spectrometry (GC-MS) based metabolomics efforts, we collectively obtained quantitative data on 177 metabolites that were derivatized (either derivatized singly or multiple times) or not representing 139 non-redundant (unique) metabolites. Out of these 139 metabolites, 118 were associated with a unique HMDB identifier, while 113 were associated with a KEGG identifier. Relative quantification of these metabolites across the time-course of umbelliferone treatment, revealed 22 compounds (sugars, fatty acids, secondary metabolites, organic acids, and amino acids) that changed significantly (repeated measures ANOVA, P-value < 0.05) with time. Using multivariate partial least squares discriminant analysis (PLS-DA) we showed the grouping of samples based on time-course across the control and umbelliferone treated plants, whereas the metabolite-metabolite Pearson correlation revealed tightly formed clusters of umbelliferone-derived metabolites, fatty acids, amino acids, and carbohydrates. Also, time-course of umbelliferone treatment revealed, that phospho-L-serine, maltose, and dehydroquinic acid were the top three metabolites showing highest importance in discrimination among the time-points. The above indicate a system-wide changes induced by umbelliferone, through dysregulation of primary as well as specialized metabolism.
INSTITUTE
Università Mediterranea di Reggio Calabria
DEPARTMENT
Dipartimento AGRARIA
LAST_NAME
Araniti
FIRST_NAME
Fabrizio
ADDRESS
Department AGRARIA, University Mediterranea of Reggio Calabria, Località Feo di Vito, SNC I-89124, Reggio Calabria RC, Italy
Metabolite Extractions data from the Strains Synechococcus sp. PCC 7002, Synechococcus elongatus PCC 11801 (New strain, Manuscript submitted) and Synechococcus elongatus PCC 7942
Lipidomics for wildlife disease etiology and biomarker discovery: a case study of pansteatitis outbreak in South Africa (part-II)
STUDY_TYPE
lipidomics
STUDY_SUMMARY
Lipidomics is a promising tool to determine biomarkers and elucidate mechanisms associated with anthropogenic-induced stress in wildlife. Therefore, we examine the application of lipidomics for in situ studies on Mozambique tilapia (Oreochromis mossambicus) in Loskop Dam, South Africa. Mortality events of aquatic life associated with an environmentally-derived inflammatory disease, pansteatitis, have occurred in this area. The lipidome of adipose tissue (n = 31) and plasma (n = 51) from tilapia collected from at Loskop Dam were characterized using state of the art liquid chromatography coupled to high-resolution tandem mass spectrometry. Lipid profiles reflected pansteatitis severity and were significantly different between diseased and healthy individuals. Over 13 classes of lipids associated with inflammation, cell death, and/or oxidative damage were upregulated in pansteatitis-affected adipose tissue, including ether-lipids, short-chained triglyceride oxidation products, sphingolipids, and acylcarnitines. Ceramides showed a 1000-fold increase in the most affected adipose tissues, illustrating its potential as sensitive and novel indicators of disease severity. In plasma, triglycerides were found to be downregulated in pansteatitis-affected tilapia. As comprehensive coverage of the lipidome aids in the elucidation of possible disease mechanisms, application of lipidomics could be applied to the understanding of other environmentally-derived inflammatory conditions, such as those caused by obesogens.
INSTITUTE
South East Center for Integrated Metabolomics
DEPARTMENT
Department of Pathology, Immunology and Laboratory Medicine
LABORATORY
SECIM
LAST_NAME
Koelmel
FIRST_NAME
Jeremy
ADDRESS
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, 1395 Center Dr, Room M641c
Glutathione (GSH) is a tripeptide that is implicated in various crucial physiological processes including redox buffering and protection against heavy metal toxicity. GSH is abundant in plants, with reported intracellular concentrations typically in the 1-10 millimolar range. Various aminotransferases can inadvertently transaminate the amino group of the γ-glutamyl moiety of GSH to produce deaminated glutathione (dGSH), a metabolite damage product. It was recently reported that an amidase known as Nit1 participates in dGSH breakdown in mammals and yeast. Plants have a hitherto uncharacterized homolog of the Nit1 amidase. We show that recombinant Arabidopsis Nit1 (At4g08790) has efficient amidase activity towards dGSH. Ablating the Arabidopsis Nit1 gene causes a massive accumulation of dGSH and other marked changes to the metabolome. All plant Nit1 sequences examined had predicted plastidial targeting peptides with a potential second start codon whose use would eliminate the targeting peptide. In vitro transcription/translation assays show that both potential translation start codons were used and subcellular localization of GFP fusions confirmed both cytosolic and plastidial localization. Further, we show that Arabidopsis enzymes convert GSH to dGSH at a rate of 2.8 pmol min-1 mg-1 in vitro. Our data demonstrate that plants have a dGSH repair system that is directed to at least two subcellular compartments via the use of alternative translation start sites.
The proteomic and metabolomic characterization of exercise-induced sweat (part -I)
STUDY_SUMMARY
Proteomic and Metabolomic analysis of exercise-induced sweat to evaluate analyte correlation with human performance parameters. Sweat was collected from participants on a treadmill at low, medium, and hard speed and incline. Sweat was analyzed by untagged HILIC LC-MS.
INSTITUTE
UES Inc, Air Force Research Laboratory
LAST_NAME
Harshman
FIRST_NAME
Sean
ADDRESS
2510 Fifth Street, Area B, Building 840, WPAFB, OH 45433
Evaluation of Seryl-leucine core 1 O-glycosylated peptide (SLC1G) in TB patient urine
STUDY_SUMMARY
Previous work detected an uncharacterized urine metabolite with a molecular mass of 874.3547 Da that showed promise as a biomarker for successful TB treatment. Using mass spectrometry combined with enzymatic digestions, the metabolite was structurally characterized as a seryl-leucine core 1 O-glycosylated peptide (SLC1G) of human origin. Examination of SLC1G in urine revealed a significant abundance increase in individuals with active TB versus their household contacts and healthy controls. Moreover, differential decreases in SLC1G levels were observed by week-one in TB patients during successful treatment versus those that failed treatment. The SLC1G levels also associated with clinical parameters used to measure bacterial burden (GeneXpert) and inflammation (PET-CT). These results demonstrate the importance of metabolite identification and provide strong evidence for applying SLC1G as a biomarker of TB treatment response.
Treatment comparison of Guinea grass planted at University of Sao Paulo Brazil 4 Ambient temp and CO2 plots, 4 elevated CO2 (600 ppm) plots, 4 elevated Temp plots (+2C),4 elevated CO2 and Temp plots. Untargeted metabolomics(GC-MS),de novo transcriptomics, and RNAseq taken at 30(A)(2014-05-22) and 50(B)(2014-07-14)days post treatment exposure. Dried leaf material sent to Uni Illinois-UC. GC-MS protocol followed as stated in Ulanov et al. (2010) J of Plant Phys.
INSTITUTE
University of Illinois at Urbana-Champaign (UIUC)
DEPARTMENT
Plant Biology
LABORATORY
Ainsworth USDA ARS Global Change and Photosynthesis Research Unit
Lipid profiling of Wnt3a-induced optic nerve regeneration
STUDY_TYPE
untargeted lipid profiling
STUDY_SUMMARY
We analyzed lipid profiles of mouse retina and optic nerve for 2 time points - 7 and 15 days post-crush, and 3 conditions - intact control, optic nerve crush + vehicle (saline) intravitreal injection, optic nerve crush + 20 ng of Wnt3a injection.
INSTITUTE
University of Miami
DEPARTMENT
Ophthalmology, Bascom Palmer Eye Institute
LABORATORY
Sanjoy K. Bhattacharya lab
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
Bascom Palmer Eye Institute (McKnight Bldg.), 1638 NW 10th Avenue, Suite 707A, University of Miami, Miami, FL, 33136
Integrated metabolome and transcriptome analyses provide novel insight into colon cancer modulation by the gut microbiota
STUDY_SUMMARY
Colon cancer onset and progression is strongly associated with the presence, absence, or relative abundances of certain microbial taxa in the gastrointestinal tract. However, specific mechanisms affecting disease susceptibility related to complex commensal bacterial mixtures are poorly understood. We used a multi-omics approach to determine how differences in the complex gut microbiome (GM) influence the metabolome and host transcriptome and ultimately affect susceptibility to adenoma development. Fecal samples collected from a preclinical rat model of colon cancer harboring distinct complex GMs were analyzed using ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). We collected samples prior to observable disease onset and identified putative metabolite profiles that predicted future disease severity, independent of GM status. Transcriptome analyses performed after disease onset from normal epithelium and tumor tissues between the high and low tumor GMs suggests that the GM is also correlated with altered host gene expression. Integrated pathway (IP) analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis was enriched in rats with high tumors (GM:F344) along with increased fatty acid metabolism and mucin biosynthesis. These data emphasize the utility of using untargeted metabolomics to reveal signatures of susceptibility and resistance and integrated analysis reveals common pathways that are likely to be universal targets for intervention.
Dynamic labeling of intracellular metabolites in PCC 7002
STUDY_TYPE
Timecourse experiment
STUDY_SUMMARY
The experiment was conducted in a reactor at a metabolic steady state (OD 730 nm = 0.8). 13C labeled sodium bicarbonate was used as a tracer. Tracer concentration was 1 g/L. After the introduction of the tracer, the samples were collected at time point : 0, 60, 120, 180 and 240 secs. Samples were quenched with methanol and extracted using methanol-chloroform-water method. Extracts were stored at -80 degree C till LCMS analysis.
Combined NMR and MS Analysis of PC patien serum (part-II)
STUDY_SUMMARY
Serum of two groups of patients were analyzed using MS and NMR to find predictive markers of recurrence. Factor Sample Type in study design section refers to samples with Recurrence (R)/ No Recurrence (NR)/ Blank (B) / Pooled (P).